<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with MathML3 v1.3 20210610//EN"  "JATS-archivearticle1-3-mathml3.dtd"><article xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article" dtd-version="1.3"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic" pub-type="epub">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">95528</article-id><article-id pub-id-type="doi">10.7554/eLife.95528</article-id><article-id pub-id-type="doi" specific-use="version">10.7554/eLife.95528.3</article-id><article-version article-version-type="publication-state">version of record</article-version><article-categories><subj-group subj-group-type="display-channel"><subject>Research Article</subject></subj-group><subj-group subj-group-type="heading"><subject>Neuroscience</subject></subj-group></article-categories><title-group><article-title>High-resolution awake mouse fMRI at 14 tesla</article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Hike</surname><given-names>David</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0001-5294-1767</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="equal-contrib1">†</xref><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Liu</surname><given-names>Xiaochen</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0001-6342-7704</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="equal-contrib1">†</xref><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Xie</surname><given-names>Zeping</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Bei</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Choi</surname><given-names>Sangcheon</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0001-7327-1344</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Xiaoqing Alice</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con6"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Andy</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0009-0004-0080-8429</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="fn" rid="con7"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Murstein</surname><given-names>Alyssa</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="fn" rid="con8"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Yuanyuan</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0001-7758-7450</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con9"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Devor</surname><given-names>Anna</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0002-5143-3960</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="other" rid="fund6"/><xref ref-type="fn" rid="con10"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Yu</surname><given-names>Xin</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0001-9890-5489</contrib-id><email>xyu9@mgh.harvard.edu</email><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="other" rid="fund1"/><xref ref-type="other" rid="fund2"/><xref ref-type="other" rid="fund3"/><xref ref-type="other" rid="fund4"/><xref ref-type="other" rid="fund5"/><xref ref-type="other" rid="fund7"/><xref ref-type="other" rid="fund8"/><xref ref-type="other" rid="fund9"/><xref ref-type="fn" rid="con11"/><xref ref-type="fn" rid="conf2"/></contrib><aff id="aff1"><label>1</label><institution-wrap><institution-id institution-id-type="ror">https://ror.org/002pd6e78</institution-id><institution>Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital</institution></institution-wrap><addr-line><named-content content-type="city">Charlestown</named-content></addr-line><country>United States</country></aff><aff id="aff2"><label>2</label><institution-wrap><institution-id institution-id-type="ror">https://ror.org/05qwgg493</institution-id><institution>Graduate Program in Neuroscience, Boston University</institution></institution-wrap><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff><aff id="aff3"><label>3</label><institution-wrap><institution-id institution-id-type="ror">https://ror.org/05qwgg493</institution-id><institution>Department of Biomedical Engineering, Boston University</institution></institution-wrap><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Lerch</surname><given-names>Jason P</given-names></name><role>Reviewing Editor</role><aff><institution-wrap><institution-id institution-id-type="ror">https://ror.org/052gg0110</institution-id><institution>University of Oxford</institution></institution-wrap><country>United Kingdom</country></aff></contrib><contrib contrib-type="senior_editor"><name><surname>Moore</surname><given-names>Tirin</given-names></name><role>Senior Editor</role><aff><institution-wrap><institution-id institution-id-type="ror">https://ror.org/006w34k90</institution-id><institution>Stanford University, Howard Hughes Medical Institute</institution></institution-wrap><country>United States</country></aff></contrib></contrib-group><author-notes><fn fn-type="con" id="equal-contrib1"><label>†</label><p>These authors contributed equally to this work</p></fn></author-notes><pub-date publication-format="electronic" date-type="publication"><day>09</day><month>01</month><year>2025</year></pub-date><volume>13</volume><elocation-id>RP95528</elocation-id><history><date date-type="sent-for-review" iso-8601-date="2024-01-22"><day>22</day><month>01</month><year>2024</year></date></history><pub-history><event><event-desc>This manuscript was published as a preprint.</event-desc><date date-type="preprint" iso-8601-date="2023-12-09"><day>09</day><month>12</month><year>2023</year></date><self-uri content-type="preprint" xlink:href="https://doi.org/10.1101/2023.12.08.570803"/></event><event><event-desc>This manuscript was published as a reviewed preprint.</event-desc><date date-type="reviewed-preprint" iso-8601-date="2024-03-28"><day>28</day><month>03</month><year>2024</year></date><self-uri content-type="reviewed-preprint" xlink:href="https://doi.org/10.7554/eLife.95528.1"/></event><event><event-desc>The reviewed preprint was revised.</event-desc><date date-type="reviewed-preprint" iso-8601-date="2024-12-09"><day>09</day><month>12</month><year>2024</year></date><self-uri content-type="reviewed-preprint" xlink:href="https://doi.org/10.7554/eLife.95528.2"/></event></pub-history><permissions><copyright-statement>© 2024, Hike, Liu et al</copyright-statement><copyright-year>2024</copyright-year><copyright-holder>Hike, Liu et al</copyright-holder><ali:free_to_read/><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><ali:license_ref>http://creativecommons.org/licenses/by/4.0/</ali:license_ref><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife-95528-v1.pdf"/><self-uri content-type="figures-pdf" xlink:href="elife-95528-figures-v1.pdf"/><abstract><p>High-resolution awake mouse functional magnetic resonance imaging (fMRI) remains challenging despite extensive efforts to address motion-induced artifacts and stress. This study introduces an implantable radio frequency (RF) surface coil design that minimizes image distortion caused by the air/tissue interface of mouse brains while simultaneously serving as a headpost for fixation during scanning. Furthermore, this study provides a thorough acclimation method used to accustom animals to the MRI environment minimizing motion-induced artifacts. Using a 14 T scanner, high-resolution fMRI enabled brain-wide functional mapping of visual and vibrissa stimulation at 100 µm×100 µm×200 µm resolution with a 2 s per frame sampling rate. Besides activated ascending visual and vibrissa pathways, robust blood oxygen level-dependent (BOLD) responses were detected in the anterior cingulate cortex upon visual stimulation and spread through the ventral retrosplenial area (VRA) with vibrissa air-puff stimulation, demonstrating higher-order sensory processing in association cortices of awake mice. In particular, the rapid hemodynamic responses in VRA upon vibrissa stimulation showed a strong correlation with the hippocampus, thalamus, and prefrontal cortical areas. Cross-correlation analysis with designated VRA responses revealed early positive BOLD signals at the contralateral barrel cortex (BC) occurring 2 s prior to the air-puff in awake mice with repetitive stimulation, which was not detected using a randomized stimulation paradigm. This early BC activation indicated a learned anticipation through the vibrissa system and association cortices in awake mice under continuous exposure of repetitive air-puff stimulation. This work establishes a high-resolution awake mouse fMRI platform, enabling brain-wide functional mapping of sensory signal processing in higher association cortical areas.</p></abstract><kwd-group kwd-group-type="author-keywords"><kwd>fMRI</kwd><kwd>BOLD</kwd><kwd>prediction</kwd><kwd>visual stimulation</kwd><kwd>vibrissa stimulation</kwd><kwd>awake mouse</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd>Mouse</kwd></kwd-group><funding-group><award-group id="fund1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>RF1NS113278</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>RF1NS124778</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>R01NS122904</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund4"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>R01NS120594</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund5"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>R21NS121642</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund6"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>U19NS123717</award-id><principal-award-recipient><name><surname>Devor</surname><given-names>Anna</given-names></name></principal-award-recipient></award-group><award-group id="fund7"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000052</institution-id><institution>NIH Office of the Director</institution></institution-wrap></funding-source><award-id>S10OD028616</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund8"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000097</institution-id><institution>National Center for Research Resources</institution></institution-wrap></funding-source><award-id>S10RR025563</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><award-group id="fund9"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000001</institution-id><institution>National Science Foundation</institution></institution-wrap></funding-source><award-id>2123970</award-id><principal-award-recipient><name><surname>Yu</surname><given-names>Xin</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>High-resolution blood oxygen level-dependent functional magnetic resonance imaging enables brain-wide mapping of activated regions during sensory stimulation in awake mice, including associated areas, for high-order sensory processing including anticipation responses.</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>publishing-route</meta-name><meta-value>prc</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>Functional magnetic resonance imaging (fMRI) indirectly measures brain activity via MRI contrast associated with endogenous blood oxygen level-dependent (BOLD) signals (<xref ref-type="bibr" rid="bib91">Ogawa et al., 1990a</xref>; <xref ref-type="bibr" rid="bib92">Ogawa et al., 1990b</xref>; <xref ref-type="bibr" rid="bib70">Logothetis et al., 2001</xref>). The BOLD contrast was first described by <xref ref-type="bibr" rid="bib97">Pauling and Coryell, 1936</xref>, but it had not been utilized in anesthetized rodent MRI until 1990 (<xref ref-type="bibr" rid="bib91">Ogawa et al., 1990a</xref>; <xref ref-type="bibr" rid="bib92">Ogawa et al., 1990b</xref>). The power of BOLD-fMRI was later revealed in human brain functional mapping (<xref ref-type="bibr" rid="bib93">Ogawa et al., 1992</xref>; <xref ref-type="bibr" rid="bib61">Kwong et al., 1992</xref>; <xref ref-type="bibr" rid="bib8">Bandettini et al., 1992</xref>) and has revolutionized cognitive neuroscience. In contrast to human studies, preclinical fMRI has played a crucial role in method development and validation (<xref ref-type="bibr" rid="bib70">Logothetis et al., 2001</xref>; <xref ref-type="bibr" rid="bib147">Zhou et al., 2023</xref>; <xref ref-type="bibr" rid="bib140">Yu et al., 2016</xref>; <xref ref-type="bibr" rid="bib138">Yoshida et al., 2016</xref>; <xref ref-type="bibr" rid="bib99">Pérez-Cervera et al., 2018</xref>; <xref ref-type="bibr" rid="bib102">Pirttimäki et al., 2016</xref>; <xref ref-type="bibr" rid="bib4">Arbabi et al., 2022</xref>; <xref ref-type="bibr" rid="bib62">Labbé et al., 2021</xref>). fMRI of anesthetized rodents reduces confounding artifacts due to motion and detects robust BOLD or cerebral blood volume signals under various anesthetics (<xref ref-type="bibr" rid="bib84">Masamoto et al., 2007</xref>; <xref ref-type="bibr" rid="bib58">Kawazoe et al., 2022</xref>; <xref ref-type="bibr" rid="bib11">Bukhari et al., 2018</xref>; <xref ref-type="bibr" rid="bib122">Steiner et al., 2021</xref>; <xref ref-type="bibr" rid="bib116">Shim et al., 2018</xref>; <xref ref-type="bibr" rid="bib53">Jonckers et al., 2014</xref>; <xref ref-type="bibr" rid="bib129">Tsurugizawa and Yoshimaru, 2021</xref>; <xref ref-type="bibr" rid="bib10">Bukhari et al., 2017</xref>; <xref ref-type="bibr" rid="bib40">Grandjean et al., 2014</xref>; <xref ref-type="bibr" rid="bib9">Becq et al., 2020</xref>; <xref ref-type="bibr" rid="bib22">Conzen et al., 1992</xref>; <xref ref-type="bibr" rid="bib79">Magnuson et al., 2014</xref>; <xref ref-type="bibr" rid="bib144">Zhao et al., 2008</xref>; <xref ref-type="bibr" rid="bib15">Chen et al., 2019b</xref>; <xref ref-type="bibr" rid="bib134">Wang et al., 2018b</xref>). Recently, the bridging power of preclinical fMRI for basic mechanistic and translational studies has been further exploited given the combination of rodent fMRI with genetic modification tools (e.g. optogenetics, chemogenetics, and genetically encoded biosensors) (<xref ref-type="bibr" rid="bib147">Zhou et al., 2023</xref>; <xref ref-type="bibr" rid="bib56">Jung et al., 2021</xref>; <xref ref-type="bibr" rid="bib24">Cover et al., 2021</xref>; <xref ref-type="bibr" rid="bib110">Rocchi et al., 2022</xref>; <xref ref-type="bibr" rid="bib66">Lee et al., 2022b</xref>; <xref ref-type="bibr" rid="bib143">Zerbi et al., 2019</xref>; <xref ref-type="bibr" rid="bib39">Giorgi et al., 2017</xref>; <xref ref-type="bibr" rid="bib112">Schulz et al., 2012</xref>; <xref ref-type="bibr" rid="bib51">Ioanas et al., 2022</xref>; <xref ref-type="bibr" rid="bib57">Jung, 2022</xref>; <xref ref-type="bibr" rid="bib14">Chen et al., 2019a</xref>; <xref ref-type="bibr" rid="bib65">Lee et al., 2022a</xref>; <xref ref-type="bibr" rid="bib88">Nakamura et al., 2020</xref>; <xref ref-type="bibr" rid="bib98">Peeters et al., 2020</xref>; <xref ref-type="bibr" rid="bib95">Oyarzabal et al., 2022</xref>). Among the many efforts in anesthetized rodent fMRI, mouse fMRI set a foundation for mechanistic multi-modal imaging given its global mapping scheme in genetic modification models (<xref ref-type="bibr" rid="bib58">Kawazoe et al., 2022</xref>; <xref ref-type="bibr" rid="bib116">Shim et al., 2018</xref>; <xref ref-type="bibr" rid="bib139">You et al., 2021</xref>; <xref ref-type="bibr" rid="bib63">Lake et al., 2020</xref>), as well as the ability to perform viral transfections to circuit- or cellular-specific targets in transgenic models. However, anesthetics alter brain function during fMRI, preventing accurate interpretation of brain functional changes in awake states (<xref ref-type="bibr" rid="bib84">Masamoto et al., 2007</xref>; <xref ref-type="bibr" rid="bib53">Jonckers et al., 2014</xref>; <xref ref-type="bibr" rid="bib40">Grandjean et al., 2014</xref>; <xref ref-type="bibr" rid="bib22">Conzen et al., 1992</xref>; <xref ref-type="bibr" rid="bib79">Magnuson et al., 2014</xref>; <xref ref-type="bibr" rid="bib29">Desai et al., 2011</xref>; <xref ref-type="bibr" rid="bib16">Chen et al., 2020</xref>; <xref ref-type="bibr" rid="bib114">Sharp et al., 2015</xref>; <xref ref-type="bibr" rid="bib72">Low et al., 2016a</xref>; <xref ref-type="bibr" rid="bib38">Gargiulo et al., 2012</xref>; <xref ref-type="bibr" rid="bib111">Scheller et al., 1988</xref>; <xref ref-type="bibr" rid="bib27">Crawford et al., 1992</xref>).</p><p>Awake mouse fMRI presents itself to provide the most relevant brain functional mapping information for translational cross-scale brain dynamic studies. To immobilize the mouse head during scanning, surgical implantation of headposts has been developed for head-fixation similar to optical imaging schemes (<xref ref-type="bibr" rid="bib138">Yoshida et al., 2016</xref>; <xref ref-type="bibr" rid="bib30">Desjardins et al., 2019</xref>; <xref ref-type="bibr" rid="bib115">Shih et al., 2014</xref>). In contrast to the fMRI mapping of anesthetized animals, motion-induced artifacts and potential stress-related issues caused by loud gradient noises and micro-vibrations during scanning are major difficulties faced by existing awake mouse fMRI studies (<xref ref-type="bibr" rid="bib29">Desai et al., 2011</xref>; <xref ref-type="bibr" rid="bib16">Chen et al., 2020</xref>; <xref ref-type="bibr" rid="bib42">Gutierrez-Barragan et al., 2022</xref>; <xref ref-type="bibr" rid="bib46">Han et al., 2019</xref>; <xref ref-type="bibr" rid="bib137">Xu et al., 2022</xref>; <xref ref-type="bibr" rid="bib69">Liu et al., 2020</xref>; <xref ref-type="bibr" rid="bib2">Almeida et al., 2022</xref>; <xref ref-type="bibr" rid="bib142">Zeng et al., 2022</xref>). Previous work has demonstrated that well-planned training procedures could acclimate awake mice during scanning (<xref ref-type="bibr" rid="bib46">Han et al., 2019</xref>; <xref ref-type="bibr" rid="bib78">Madularu et al., 2017b</xref>; <xref ref-type="bibr" rid="bib137">Xu et al., 2022</xref>; <xref ref-type="bibr" rid="bib69">Liu et al., 2020</xref>; <xref ref-type="bibr" rid="bib2">Almeida et al., 2022</xref>; <xref ref-type="bibr" rid="bib73">Low et al., 2016b</xref>; <xref ref-type="bibr" rid="bib19">Chiba et al., 2012</xref>; <xref ref-type="bibr" rid="bib35">Ferenczi et al., 2016</xref>); however, different training paradigms are expected to produce large variability in the functional mapping results (<xref ref-type="bibr" rid="bib80">Mandino et al., 2024</xref>). One ongoing challenge of awake mouse fMRI is to provide reproducible and high-quality brain functional images with sufficient spatiotemporal resolution and signal-to-noise ratio (SNR) to distinguish functional nuclei of only a few hundred microns in mouse brains. Since increasing spatiotemporal resolution leads to a reduction in SNR of the images, accessing the highest field MRI available, as well as maximizing the efficiency of the radio frequency (RF) transceiver signal is critical. Although cryoprobes have been well implemented to boost SNR (<xref ref-type="bibr" rid="bib138">Yoshida et al., 2016</xref>; <xref ref-type="bibr" rid="bib16">Chen et al., 2020</xref>; <xref ref-type="bibr" rid="bib89">Niendorf et al., 2015</xref>), construction limitations of the superconducting environment constrain the usable space and flexibility to accommodate other imaging/recording modalities (<xref ref-type="bibr" rid="bib138">Yoshida et al., 2016</xref>; <xref ref-type="bibr" rid="bib4">Arbabi et al., 2022</xref>; <xref ref-type="bibr" rid="bib7">Baltes et al., 2009</xref>; <xref ref-type="bibr" rid="bib135">Wright et al., 2000</xref>; <xref ref-type="bibr" rid="bib60">Kwok and You, 2006</xref>; <xref ref-type="bibr" rid="bib124">Takata et al., 2015</xref>; <xref ref-type="bibr" rid="bib1">Abe et al., 2021</xref>; <xref ref-type="bibr" rid="bib45">Hamada, 2024</xref>). Implantable coils have been used in animal imaging for over three decades (<xref ref-type="bibr" rid="bib102">Pirttimäki et al., 2016</xref>; <xref ref-type="bibr" rid="bib33">Farmer et al., 1990</xref>; <xref ref-type="bibr" rid="bib123">Summers et al., 1995</xref>; <xref ref-type="bibr" rid="bib71">Logothetis et al., 2002</xref>; <xref ref-type="bibr" rid="bib133">Wang et al., 2018a</xref>; <xref ref-type="bibr" rid="bib67">Lee et al., 2024</xref>; <xref ref-type="bibr" rid="bib77">Madularu et al., 2017a</xref>; <xref ref-type="bibr" rid="bib17">Chen et al., 2022</xref>). Their use gained popularity due to higher SNR and reduction of susceptibility artifacts. The main limitation of implantable coils is the need to surgically implant these coils, adding a degree of invasiveness that MRI usually avoids. However, for typical awake mouse neuroimaging studies, surgical procedures to provide a head-fixation apparatus are routinely practiced. Replacing the conventional headpost for immobilization of the head with an implantable RF coil is critical for achieving high-resolution awake mouse fMRI using ultra-high field MRI, e.g., 14 T shown here.</p><p>In this present study, we established an awake mouse fMRI platform by applying an implantable RF surface coil, permanently affixed to the head, which simultaneously functioned as a headpost for fixation during scanning, minimizing animal motion. This setup allowed us to acquire images with an in-plane spatial resolution of 100 µm and 200 µm slice thickness. This unique implantable RF coil/headpost scheme simplified the awake mouse training and conditioning for imaging. While there is currently insufficient evidence to ascertain whether head-fixed training leads to stress-free animals, we observed that a 5-week training scheme resulted in increased eye movements, presenting decreased struggling and freezing behavior indicative of calmer awake mice during scanning. This implanted RF coil scheme also improved B<sub>0</sub> homogeneity, as well as effectively eliminated any motion-related loading changes causing B<sub>1</sub> variability. Here, we successfully mapped activated visual and vibrissa pathways and detected robust BOLD responses in higher-order association cortices, e.g., anterior cingulate area (ACA) with visual stimulation and ventral retrosplenial area (VRA) with vibrissa stimulation in awake mice based on connectivity map projections from the Allen Brain Atlas derived from a Cre-dependent AAV tracing of axonal projections (<xref ref-type="bibr" rid="bib94">Oh et al., 2014</xref>). Interestingly, the repetitive vibrissa stimulation paradigm in awake mice has enabled us to detect potential anticipatory learning with mice predicting the onset of stimulation. Our work is a fundamental step toward combining high-resolution fMRI with other modalities to simultaneously record neuronal and microvascular signals throughout brain-wide circuity in awake mice.</p></sec><sec id="s2" sec-type="methods"><title>Methods</title><sec id="s2-1"><title>Animals</title><p>Thirty-eight C57BL/6 mice were used in the current study (weighing between 20 g and 30 g) and allocated as follows for each experiment: SNR measurements at 9.4 T – 16 male mice; SNR, visual, and whisker stimulation measurements at 14 T – 13 mice (6F/7M); random stimulation measurements at 14 T – 9 mice (4F/5M). Mice were group-housed (3–4/cage) under a 12 hr light/dark cycle with food and water ad libitum. All animal procedures were conducted in accordance with protocols approved by the Massachusetts General Hospital (MGH) Institutional Animal Care and Use Committee (IACUC) under protocol number 2020N000073, and animals were cared for according to the requirements of the National Research Council’s Guide for the Care and Use of Laboratory Animals.</p></sec><sec id="s2-2"><title>Awake mouse fMRI setup</title><p>The awake mouse cradle was designed in Blender (Blender Foundation, Amsterdam, NL) and 3D printed using a Formlabs 3L 3D printer (Formlabs Inc, Somerville, MA, USA). The design incorporated a sliding track which accepted the printed circuit board (PCB) chip transceiver circuit to slide in while the mouse was inserted into the cradle. Two transceiver circuit designs were built, a single loop and a ‘figure 8’ design. Each one keeps the B<sub>1</sub> direction orthogonal to the B<sub>0</sub>. The single loop allows for full brain coverage at sufficient depths for subcortical investigation. The ‘figure 8’ design, due to its smaller coil loops and B<sub>1</sub> direction, is limited to precise measurements of shallow brain regions but provides a significant increase in SNR which is beneficial to cortical-specific studies which do not have a need to look deeper into subcortical regions but would benefit from a much higher SNR. The single loop or ‘figure 8’ shape RF coils were built to optimize tuning/matching performance when affixed onto the mouse skull. The coils serve to optimize the B<sub>0</sub> homogeneity by minimizing the air-tissue interface. Each coil was built to weigh ~2.5 g minimizing the recovery/neck strengthening time of each mouse. The standardized RF coil was acquired from MRIBOT LLC (Malden, MA, USA) using the circuit diagram shown in <xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>.</p></sec><sec id="s2-3"><title>Animal surgery</title><p>Mice underwent surgery to affix the RF coil to the head. Animals were anesthetized for surgery using isoflurane. Induction was accomplished using 5% isoflurane and 1 L/min of medical air and 0.2 L/min additional O<sub>2</sub> flow. Animals were maintained at 1.5–2% isoflurane using respiration rate as a monitor for anesthesia depth. To attach the head coil, mice were affixed in a stereotaxic stage to stabilize the head with ear and bite bars. The scalp was shaved sterilized with ethanol and iodine and an incision was made to expose an area of the skull the size of the RF coil ring. The skull was cleared of residual tissue and cleaned with 0.3% H<sub>2</sub>O<sub>2</sub> and PBS before being dried. The coil was then positioned over the skull covering the underlying brain. The coil ring was lifted ~0.3–0.5 mm above the surface of the skull to avoid over-loading effects and held in place while a thin layer of cyanoacrylate glue was applied to connect the coil to the skull. Once dried (~5–8 min), two-part dental cement (Stoelting Co., Wood Dale, IL, USA) was mixed and applied to cover the coil and exposed bone paying special note to the base of the coil to firmly secure it and avoid air bubbles and drips toward the eyes. The edges of the skin were then glued to close the surgical site. After the dental cement had fully hardened (~10 min), the mouse was released from the stereotaxic stage and received subcutaneous injections of dexamethasone and cefazolin. Mice were then allowed to recover in their home cage for at least 1 week to ensure ample neck strengthening had occurred and the mice could walk with normal head posture.</p></sec><sec id="s2-4"><title>Animal training</title><p>To acclimate the animals to the MRI environment, each mouse underwent 5 weeks of intermittent habituation procedures to train animals before fMRI experiments by using the following method:</p><p>Training days pre-surgery (Phase 1)</p><list list-type="order"><list-item><p>in hand mouse handling → 5 min</p></list-item><list-item><p>in hand mouse handling → 10 min</p></list-item></list><p>Holder training days post-surgery (after recovery) (Phase 2)</p><list list-type="order"><list-item><p>secured in holder → 15 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder → 30 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item></list><p>Mock-MRI training days (Phase 3)</p><list list-type="order"><list-item><p>secured in holder with MRI audio → 30 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 30 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 30 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 30 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 60 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 60 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 60 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording after</p></list-item></list></list-item><list-item><p>secured in holder with MRI audio → 60 min</p><list list-type="alpha-lower"><list-item><p>10 min pupil recording</p></list-item></list></list-item></list><p>Training days inside MRI (resting-state and stimulation) (Phase 4)</p><list list-type="order"><list-item><p>Real scans (EPI with pupil recording)</p></list-item><list-item><p>Real scans (EPI with pupil recording)</p></list-item><list-item><p>Real scans (EPI with air-puff and pupil recording)</p></list-item><list-item><p>Real scans (EPI with air-puff and pupil recording)</p></list-item></list><p>Following this, data acquisition began, and pupil changes were monitored during scans. During all pupil recordings, animals were secured in the holder and ensured the environment for recording did not allow external light to reach the pupil. Illumination was achieved from a 660 nm LED light source (Thorlabs, Inc, Newton, NJ, USA) delivered via fiber-optic cable. Videos were captured at 30 fps using a 1/3” CMOS camera and 12 mm focal length lens (Tru Components, Chicago, IL, USA).</p></sec><sec id="s2-5"><title>Pupil/eye fluctuations during training regime</title><p>The pupils of awake mice were recorded during training sessions, allowing investigation into eye movements and pupil diameter changes as potential surrogate of stress-related readouts of the animals. The pupil recordings were measured over 12 training days across 3–4 weeks in Phases 2–4 (<xref ref-type="table" rid="table1">Table 1</xref>). In Phase 1, animals were gently held in hands, not head-fixed in the cradle. In the second half of Phase 4, head-fixed animals were exposed to air-puff stimulation inside the MR scanner during echo planar imaging (EPI) sequences acquisition. At this stage, animals tended to close their eyes in response to air-puff, so pupil measurements were not feasible to be included for data analysis. The increased eye movements were well detected in Phase 3 when animals were exposed to the real MRI acoustic noise in the head-fixed position (located in the RF shielded box attached to the 14 T magnet, i.e. the CCM box) (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplement 1A</xref>). Interestingly, in Phase 4, animals showed significantly reduced eye movements during the first day when animals were positioned inside the MR scanner with EPI scanning, while an increase in eye movement went back to the level of Phase 3 in the following training days. The pupil diameter changes were also measured as the function of training days. The power spectral analysis showed ultra-slow pupil dynamic changes with peaked bandwidths less than 0.02 Hz. Interestingly, the power of the ultra-slow pupil dynamics also increased as the function of time similar to eye movements, in particular, during Phase 3. Meanwhile, power reduction in the first day of in-bore training followed with recovered pupil dynamics in the following days was also observed during Phase 4. Although the actual stress of the animals during scanning remains to be further investigated following the 5-week training procedure, the motion-induced image distortion has been dramatically reduced in well-trained animals compared to the start of in-bore training.</p><table-wrap id="table1" position="float"><label>Table 1.</label><caption><title>Table showing the training paradigm for each of the four phases of training.</title><p>rs → resting-state fMRI, stim → whisker stimulation fMRI.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="bottom">Training day of phase</th><th align="left" valign="bottom">Phase 1(hold in hand)</th><th align="left" valign="bottom">Phase 2(holder+pupil)</th><th align="left" valign="bottom">Phase 3(mock-MRI+pupil)</th><th align="left" valign="bottom">Phase 4(EPI+pupil)</th></tr></thead><tbody><tr><td align="left" valign="bottom"><bold>1</bold></td><td align="left" valign="bottom">5 min</td><td align="left" valign="bottom">15 min</td><td align="left" valign="bottom">30 min</td><td align="left" valign="bottom">60 min (rs)</td></tr><tr><td align="left" valign="bottom"><bold>2</bold></td><td align="left" valign="bottom">10 min</td><td align="left" valign="bottom">30 min</td><td align="left" valign="bottom">30 min</td><td align="left" valign="bottom">60 min (rs)</td></tr><tr><td align="left" valign="bottom"><bold>3</bold></td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">30 min</td><td align="left" valign="bottom">60 min (stim)</td></tr><tr><td align="left" valign="bottom"><bold>4</bold></td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">30 min</td><td align="left" valign="bottom">60 min (stim)</td></tr><tr><td align="left" valign="bottom"><bold>5</bold></td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 min</td><td align="left" valign="bottom"/></tr><tr><td align="left" valign="bottom"><bold>6</bold></td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 min</td><td align="left" valign="bottom"/></tr><tr><td align="left" valign="bottom"><bold>7</bold></td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 min</td><td align="left" valign="bottom"/></tr><tr><td align="left" valign="bottom"><bold>8</bold></td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 min</td><td align="left" valign="bottom"/></tr></tbody></table></table-wrap></sec><sec id="s2-6"><title>Anesthesia regiment for MRI measurements of SNR</title><p>While acquiring images to measure SNR improvements, all animals were anesthetized for the duration of MR scanning. Mice were induced using 5% isoflurane in medical air and maintained with 1.0–2.0% isoflurane, adjusted to retain stable physiological conditions while in the magnet. The gas mixture was supplied through the hollow bite bar directly to the mouth and nose of the animal at a rate of 1.0 L/min. Animals were anesthetized to minimize artifacts associated with motion. Physiological monitoring of the animal was performed through the integration of a Small Animal Monitoring and Gating System (Model 1030, SA Instruments, Inc, Stony Brook, NY, USA) capable of recording respiration, body temperature, electrocardiogram, and other parameters. The animal’s breathing rate was continuously monitored and recorded during scanning using a pressure-sensitive sensor-pad and maintained between 50 and 80 breath/min. Animals were kept at a constant temperature of 37°C in the MRI scanner by means of blowing warm air through the bore and recorded using a rectal thermometer probe.</p></sec><sec id="s2-7"><title>MRI methods</title><p><sup>1</sup>H MRI data was acquired using the 14 T and 9.4 T horizontal MRI scanners (Magnex Sci, UK) located at the Athinoula A. Martinos Center for Biomedical Imaging in Boston, MA. The 14 T magnet is equipped with a Bruker Avance Neo Console (Bruker-Biospin, Billerica, MA, USA) and is operated using ParaVision 360 V.3.3. A microimaging gradient system (Resonance Research, Inc, Billerica, MA, USA) provides a peak gradient strength of 1.2 T/m over a 60 mm diameter. The 9.4 T scanner is equipped with a Bruker Avance III HD Console (Bruker-Biospin, Billerica, MA, USA) and is operated using ParaVision 6. A dual microimaging gradient system comprises a Bruker gradient coil capable of 44 G/cm, and a Resonance Research gradient insert capable of 150 G/cm.</p><sec id="s2-7-1"><title>SNR measurements</title><p><sup>1</sup>H MRI data for SNR measurements were acquired on 9.4 T (400 MHz) and 14 T (600 MHz) scanners using the following parameters for both systems: TE/TR = 3 ms/475 ms, flip angle = 30<sup>o</sup>, and four averages for an approximate acquisition time of 4.5 min.</p><p>9.4 T scanner was only used to show SNR improvements from the implantable coils. The BOLD fMRI data were collected only at 14 T due to the much-improved SNR available and were collected solely in awake mice to investigate signal associated with the awake functional connectivity. Furthermore, the ‘figure 8’ shape coils were only used to show the SNR improvement due to the coil design for cortical measurements.</p></sec><sec id="s2-7-2"><title>fMRI BOLD imaging</title><p>Multi-slice 2D gradient echo EPI was used to acquire fMRI BOLD data from the awake animals with the following parameters: TE/TR = 7 ms/1 s, segments = 2, bandwidth = 277,777 Hz, 100 µm ×100 µm in plane resolution with a 200 µm slice thickness, 36 slices, 205 repetitions for an acquisition time of 6 min 50 s.</p></sec><sec id="s2-7-3"><title>Anatomical imaging</title><p><sup>1</sup>H MRI data for anatomical registration data were acquired using a multi-slice T<sub>1</sub>-weighted 2D gradient echo fast low angle shot (FLASH) sequence with the same parameters of the SNR measurement scans except the resolution was adjusted to match the BOLD data at 100 µm×100 µm×200 µm resolution with the parameters mentioned in the ‘SNR measurements’ subsection.</p></sec></sec><sec id="s2-8"><title>Stimulation method/paradigm</title><p>The visual and vibrissa stimulation block paradigm was designed as follows: 5 baseline scans, 1 stimulation trigger scan, 19 inter-stimulation scans, and 10 epochs. The visual stimulation used two different wavelengths of light: 530 nm and 490 nm, which flashed at 5 Hz and 5.1 Hz, respectively, for 8 s with a 20 ms ‘on’ time of each illumination. The whisker air-puff stimulation used the same block design as the visual stimulation but was stimulated with a 10 ms puff duration and an 8 Hz firing rate for 8 s. Due to the use of two segments for these experiments, the effective TR was 2 s. Therefore, the stimulation duration for both visual and vibrissa experiments resulted in four consecutive scans being included in the ‘on’ stimulation period and 16 consecutive scans being included in the ‘rest’ period (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>). The random vibrissa stimulation paradigm used the same 10 ms air-puff at 8 Hz for 8 s but randomized the ‘rest’ duration. ‘Rest’ durations were 12 s, 22 s, 32 s, and 42 s and randomized in three different sequences maintaining a scan duration of 205 TRs for each experiment.</p></sec><sec id="s2-9"><title>Processing/analysis methods (AFNI and MATLAB)</title><p>SNR was computed by dividing mean signal over the standard deviation of the noise. SNR line profile signal data was collected using Amira software (Thermo Fisher Scientific Inc, Waltham, MA, USA). fMRI data was processed using Analysis of Functional Neuroimages (AFNI) (<xref ref-type="bibr" rid="bib25">Cox, 1996</xref>; <xref ref-type="bibr" rid="bib26">Cox and Hyde, 1997</xref>). Bruker 2dseq images of the EPI and FLASH scans were converted to AFNI format using ‘to3d’ before masking and aligning the dataset to a template.</p><p>To process the high-resolution stimulated BOLD response from the visual and vibrissa stimulation paradigms, we developed a processing pipeline (<xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>). For each experiment, FLASH data were averaged for anatomical localization and the EPI scans were time averaged before registration. The time-averaged EPI was then registered to the FLASH and then to the Australian Mouse Brain Mapping Consortium (AMBMC) atlas (<xref ref-type="bibr" rid="bib52">Janke and Ullmann, 2015</xref>) where a mask was generated. Each time series for each experiment was concatenated so each experiment contains one long time series dataset using the ‘3dTcat’ command. Data were then despiked before each EPI time point was registered, via a 6-degree transformation, to the atlas using the ‘volreg’ command after which the previously generated mask was applied. The ‘blur’ command was used to smooth the newly transformed data before it was scaled and underwent a linear regression. All concatenated data was then split and summed, per each experimental study, to undergo motion correction and outlier removal. The corrected data was then summed and averaged with the remaining processed data to generate a single time series across all experiments. A clustering threshold was set at 100 voxels and the Pearson correlation values were limited to p≤0.01 (corrected) with estimated false discover rate at q=0.00078. For the random stimulation design, the three runs were concatenated into a single time series each ensuring they all followed the same series of random timings.</p></sec></sec><sec id="s3" sec-type="results"><title>Results</title><sec id="s3-1"><title>Development and efficiency validation of implantable RF coils to boost SNR</title><p>We have developed an implantable RF coil which effectively boosted the SNR in ultra-high field MRI. Here, we compared two prototypes: a simple single loop coil design and a ‘figure 8’ coil design. These coils were used to check SNR in anatomical data of anesthetized mice at 9.4 T and 14 T. <xref ref-type="fig" rid="fig1">Figure 1</xref> shows examples of the prototyped RF coils (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). The acquired SNR values for each prototype design are shown in <xref ref-type="fig" rid="fig1">Figure 1B</xref>. Here, we used a commercial four phase-array coil (400 MHz for 9.4 T) as a control to compare with the implantable RF coils. The single loop implantable coils improved SNR over 100% compared the commercial option while the ‘figure 8’ style showed a more than five times increase at 9.4 T in the cortical regions. The SNR along the dorsal-ventral axis was plotted to compare the B<sub>1</sub> field sensitivity of the single loop and ‘figure 8’ RF coils in comparison with the phase-array coil at 9.4 T, showing significantly increased SNR up to 4 mm depth (<xref ref-type="fig" rid="fig1">Figure 1B</xref>). Moving up to 14 T, the SNR improvements increased proportionally as a factor of field strength (<xref ref-type="bibr" rid="bib104">Pohmann et al., 2016</xref>). This improved SNR allows for high spatial resolution fMRI studies of awake mice. The single loop coil tuned to 14 T (600 MHz) was used for functional data collection in the manuscript. The ‘figure 8’ coil was only used as part of development to show the improvement of the coil design for cortical MR signal measurements.</p><fig-group><fig id="fig1" position="float"><label>Figure 1.</label><caption><title>Comparison between implanted and commercial coils.</title><p>(<bold>A and B</bold>) show representative (unattached) prototype coils in the single loop and ‘figure 8’ styles, respectively. (<bold>C</bold>) Box-and-whisker plot presents the cortical-specific signal-to-noise ratio (SNR) values calculated by dividing the mean signal of the upper cortex by the standard deviation of the noise to compare between commercial Bruker phased array surface coil, single loop implant, and ‘figure 8’ style implants. Bruker → commercial phased array coil, IL → implanted single loop coil, IF8 → implanted ‘figure 8’ coil. The bar graph shows the SNR of anatomical images acquired with different radio frequency (RF) coils using the 9.4 T scanner (<inline-formula><mml:math id="inf1"><mml:mstyle displaystyle="true" scriptlevel="0"><mml:mrow><mml:msub><mml:mover><mml:mrow><mml:mi>S</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi></mml:mrow><mml:mo accent="false">¯</mml:mo></mml:mover><mml:mrow><mml:mi>B</mml:mi><mml:mi>r</mml:mi><mml:mi>u</mml:mi><mml:mi>k</mml:mi><mml:mi>e</mml:mi><mml:mi>r</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mstyle></mml:math></inline-formula> = 27.2, N=6, <inline-formula><mml:math id="inf2"><mml:mstyle displaystyle="true" scriptlevel="0"><mml:mrow><mml:msub><mml:mover><mml:mrow><mml:mi>S</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi></mml:mrow><mml:mo accent="false">¯</mml:mo></mml:mover><mml:mrow><mml:mi>I</mml:mi><mml:mi>L</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mstyle></mml:math></inline-formula> = 57.5, N=5, <inline-formula><mml:math id="inf3"><mml:mstyle displaystyle="true" scriptlevel="0"><mml:mrow><mml:msub><mml:mover><mml:mrow><mml:mi>S</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi></mml:mrow><mml:mo accent="false">¯</mml:mo></mml:mover><mml:mrow><mml:mi>I</mml:mi><mml:mi>F</mml:mi><mml:mn>8</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:mstyle></mml:math></inline-formula> = 142.5, N=5) and the 14 T scanner (<inline-formula><mml:math id="inf4"><mml:mstyle displaystyle="true" scriptlevel="0"><mml:mrow><mml:msub><mml:mover><mml:mrow><mml:mi>S</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi></mml:mrow><mml:mo accent="false">¯</mml:mo></mml:mover><mml:mrow><mml:mi>I</mml:mi><mml:mi>L</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:mstyle></mml:math></inline-formula> = 96.8, N=4, <inline-formula><mml:math id="inf5"><mml:mstyle displaystyle="true" scriptlevel="0"><mml:mrow><mml:msub><mml:mover><mml:mrow><mml:mi>S</mml:mi><mml:mi>N</mml:mi><mml:mi>R</mml:mi></mml:mrow><mml:mo accent="false">¯</mml:mo></mml:mover><mml:mrow><mml:mi>I</mml:mi><mml:mi>F</mml:mi><mml:mn>8</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:mstyle></mml:math></inline-formula> = 209.2, N=5).</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig1-v1.tif"/></fig><fig id="fig1s1" position="float" specific-use="child-fig"><label>Figure 1—figure supplement 1.</label><caption><title>Schematic of circuit diagram of coil designed for <sup>1</sup>H imaging at 600 MHz.</title><p>C1 and C4 are 2.2 pF capacitors. C2 is a 0.6–2.5 pF trimmer. C3 is a 5–18 pF trimmer.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig1-figsupp1-v1.tif"/></fig><fig id="fig1s2" position="float" specific-use="child-fig"><label>Figure 1—figure supplement 2.</label><caption><title>Comparison between implanted and commercial coils.</title><p>(<bold>A</bold>) shows representative (unimplanted) coils in the single loop (left) and ‘figure 8’ styles (right). <xref ref-type="table" rid="table2">Table 2</xref> provides a parts list and cost for making these coils and <xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref> provides a circuit diagram to assemble. (<bold>B</bold>) presents the signal-to-noise ratio (SNR) line profile values as a function of distance from pia mater for each coil tested at 9.4 T: commercial phased array surface coil (four array), implanted single loop, and implanted ‘figure 8’. SNR values were calculated by dividing the signal by the standard deviation of the noise. Shaded regions represent standard error. (<bold>C–E</bold>) show a representative fast low angle shot (FLASH) image with line profile of SNR measurements from each of the coils used to create the graph seen in (<bold>B</bold>). Clear visual improvement in SNR can be seen in figures (<bold>C–E</bold>) . C – commercial phased array. D – single loop at 9.4 T. E – ‘figure 8’ at 9.4 T (N<sub>4 array</sub> = 6, N<sub>single loop</sub> = 5, N<sub>figure 8</sub> = 5).</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig1-figsupp2-v1.tif"/></fig></fig-group><table-wrap id="table2" position="float"><label>Table 2.</label><caption><title>Parts list for construction of 200 <sup>1</sup>H coils configured for 600 MHz (14 T).</title></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="top">Part description</th><th align="left" valign="top">Cost</th></tr></thead><tbody><tr><td align="left" valign="top">FR-4 PCB Chip, 0.4×0.8 in, 0.062 in thick</td><td align="left" valign="top">$214.00/200</td></tr><tr><td align="left" valign="top">Capacitor 2.2 pF 2KV</td><td align="left" valign="top">$309.80/400</td></tr><tr><td align="left" valign="top">Trimmer 0.6–2.5 pF</td><td align="left" valign="top">$1649.28/200</td></tr><tr><td align="left" valign="top">Trimmer 5–18 pF</td><td align="left" valign="top">$1640.56/200</td></tr><tr><td align="left" valign="top">Magnet wire 20AWG</td><td align="left" valign="top">$118.28/spool/710.8’</td></tr><tr><td align="left" valign="top">MCX socket</td><td align="left" valign="top">$1027.14/200</td></tr><tr><td align="left" valign="top">Entire coil built by MRIBOT</td><td align="left" valign="top">$300/each</td></tr></tbody></table></table-wrap></sec><sec id="s3-2"><title>Awake mouse fMRI with visual stimulation</title><p>The RF coil was implanted on the mouse skull to serve as an attachment for head-fixation during awake mouse fMRI at 14 T (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). The awake mouse fMRI setup was designed using a 3D printed cradle incorporating a sliding track which enabled the PCB chip mounted on the mouse head to slide through. The PCB chip was then fixed in place at the end of the cradle using friction screws (<xref ref-type="video" rid="video1">Video 1</xref>). Once the mouse was fixed in the animal cradle, either a mirror or air tube was positioned for pupillometry recording or vibrissa stimulation, respectively. Additionally, an MRI-compatible camera was incorporated to record the pupil dynamic changes and whisking behavior of awake mice during scanning. One key feature of the awake mouse fMRI setup is the plug and play capability for scanning.</p><fig-group><fig id="fig2" position="float"><label>Figure 2.</label><caption><title>High-resolution awake mouse functional magnetic resonance imaging (fMRI) at 14 T.</title><p>(<bold>A</bold>). The awake mouse setup with head-fixed position in a custom-built cradle for visual and vibrissa stimulation. (<bold>B</bold>) The representative fMRI time course of an awake mouse based on raw image data acquired from high-resolution echo planar imaging (EPI), enabling the trace of motion-induced artifacts. (<bold>C</bold>) The anatomical MRI images (fast low angle shot [FLASH]) acquired from one representative awake mouse, showing minimal susceptibility and whole brain coverage from the implanted surface coil. (<bold>D</bold>) The raw EPI fMRI image with same spatial resolution as the anatomical FLASH image. (<bold>E</bold>) The snapshot of the distorted images due to motion of the awake mouse during scanning. <xref ref-type="video" rid="video2">Video 2</xref> shows the video of motion-induced artifacts throughout the fMRI trial.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig2-v1.tif"/></fig><fig id="fig2s1" position="float" specific-use="child-fig"><label>Figure 2—figure supplement 1.</label><caption><title>Results of acclimation training on animals.</title><p>(<bold>A</bold>) Box-and-whisker plot showing eye movements over 10 min duration of training days showing an increase in eye movements over the training duration indicating the animals are becoming more relaxed in the holder while being exposed to MRI sounds. The drop in eye movements at Phase 4 Training Day 1 is caused by putting the animals into the MRI for the final training. The following day at Phase 4 Training Day 2, the eye movements have increased back to the level before being inserted into the scanner. Phase 2 incorporated the 2 days animals were put in the holder without the mock-MRI environment. Phase 3 includes each day of training in a mock-MRI environment. Phase 4 showcases eye movements acquired inside the MRI during resting-state data acquisition. (<bold>B</bold>) Box-and-whisker plot of the ratio of detectable motion during scanning +1 or 2 days after training (train) and after 1 month of scanning (real) showing a non-significant decrease in the detectable motion indicating the effectiveness of the training. (<bold>C</bold>) Graph of the normalized power spectrum density (PSD) showing the increase of low-frequency pupil oscillations from eye in each phase. (<bold>D</bold>) Box-and-whisker plot showing the averaged normalized PSD of pupil oscillation frequencies below 0.02 Hz as maximally indicated in (C) showing late stage increases in mock-MRI and EPI-MRI phases, e.g., Phase 3 and Phase 4. Circle with black dot represents the median of each data group.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig2-figsupp1-v1.tif"/></fig><fig id="fig2s2" position="float" specific-use="child-fig"><label>Figure 2—figure supplement 2.</label><caption><title>Figure showing motion data (.MOT file) of a representative mouse immediately following training (<bold>A</bold>) and after 1 month of scanning (<bold>B</bold>) indicating the amount of struggling the animal is doing during scanning.</title><p>Struggling-induced spikes are already substantially minimized following the training with only 5 volumes (2%) censored. After 1 month of scanning there was only one single repetition (repetition 204) at the end of the scan that was censored.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig2-figsupp2-v1.tif"/></fig></fig-group><media mimetype="video" mime-subtype="mp4" xlink:href="elife-95528-video1.mp4" id="video1"><label>Video 1.</label><caption><title>Video illustrating how animals are set up through the cradle using the implanted radio frequency (RF) coil for awake mouse imaging.</title></caption></media><p>This awake mouse fMRI setup enabled high-resolution EPI data acquisition at 100 µm×100 µm×200 µm spatial resolution with a 2 s effective repetition time (TR). The EPI-based T2* images acquired from head-fixed awake mice show little air-tissue interface-induced image distortion with the same spatial resolution as anatomical images (<xref ref-type="fig" rid="fig2">Figure 2C and D</xref>). Motion artifacts were detected at some time points of the fMRI time course, presenting large EPI image distortions (<xref ref-type="fig" rid="fig3">Figure 3E</xref>, <xref ref-type="video" rid="video2">Video 2</xref>), but can be removed using a censoring function during data analysis (<xref ref-type="fig" rid="fig3s2">Figure 3—figure supplement 2</xref>). These results have shown that the multi-slice 2D EPI enables brain-wide functional mapping of awake mice.</p><fig-group><fig id="fig3" position="float"><label>Figure 3.</label><caption><title>Visual stimulation-evoked high-resolution functional magnetic resonance imaging (fMRI) of awake mice.</title><p>(<bold>A</bold>) The brain-wide functional maps of awake mice show strong positive blood oxygen level-dependent (BOLD) activation in the visual cortex (VC), lateral geniculate nucleus (LGN), superior colliculus (SC), and anterior cingulate area (ACA) based on the group analysis. Highlighted brain regions are statistically generated using a one-way T-test with p&lt;0.0001 (<bold>B</bold>) The averaged time course of the ROIs derived from the Allen Brain Atlas, demonstrating an evoked positive BOLD signal changes upon the 8 s visual stimulation (5 Hz 530 nm and 5.1 Hz 490 nm 20 ms light pluses). Each graph displays the average of 162 sets of 3 stimulation epochs. Shaded regions represent standard error. Red lines represent the 8 s stimulation duration. (<bold>C</bold>) Functional maps overlain with the brain atlas to highlight the activated brains regions: VC, SC, LGN, and ACA (N=13 (6F/7M)).</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig3-v1.tif"/></fig><fig id="fig3s1" position="float" specific-use="child-fig"><label>Figure 3—figure supplement 1.</label><caption><title>Figure showing stimulation paradigm in blue.</title><p>Each ‘TR period’ is 2 s. The stimulation is repeated 10 times over the 410 s acquisition period which includes a 10 s baseline acquisition period before the first stimulation. This paradigm results in 4 ‘TR periods’ occurring during the stim on phase and 16 ‘TR periods’ occurring during the stim off phase. Any stimulation design can be used for the ‘on’ duration. TR, repetition time.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig3-figsupp1-v1.tif"/></fig><fig id="fig3s2" position="float" specific-use="child-fig"><label>Figure 3—figure supplement 2.</label><caption><title>The processing pipeline of the awake mouse functional magnetic resonance imaging (fMRI) datasets.</title><p>The workflow diagram is described through the following steps: raw data registration, outlier removal, volume registration-based motion file estimation, motion removal, linear regression with the censoring function, functional map demonstration.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig3-figsupp2-v1.tif"/></fig><fig id="fig3s3" position="float" specific-use="child-fig"><label>Figure 3—figure supplement 3.</label><caption><title>Time course from single experiment showing strong blood oxygen level-dependent (BOLD) activations during stimulation paradigm.</title><p>(Left) BOLD activation map highlighting positive activation in the barrel cortex (BC) and selection of a 3×3 voxel display of time course data (green box). (Right) Time course data taken from 3×3 voxel selection clearly showing 10 stimulations in each of the voxels shown.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig3-figsupp3-v1.tif"/></fig></fig-group><media mimetype="video" mime-subtype="mp4" xlink:href="elife-95528-video2.mp4" id="video2"><label>Video 2.</label><caption><title>Video showing the real-time EPI raw images from awake mice.</title><p>The real-time tracer from the selected point demonstrates the time points with motion, as well as the motion-induced image distortion during awake mouse fMRI.</p></caption></media><p>To map the brain function of awake mice with this high-resolution fMRI method, we first introduced a visual stimulation paradigm. Based on a block design regression analysis, we detected robust BOLD responses. Brain-wide functional maps using the visual stimulation paradigm were seen with activated areas highlighted along the visual pathways (<xref ref-type="fig" rid="fig3">Figure 3</xref>). These areas included the visual cortex (VC), superior colliculus (SC), lateral geniculate nucleus (LGN), and association cortex in the ACA. The ROI-specific localization was well characterized by overlapping the brain atlas and functional maps (<xref ref-type="fig" rid="fig3">Figure 3C</xref>). The ROI-based time courses demonstrated robust BOLD responses detected in awake mice (<xref ref-type="fig" rid="fig3">Figure 3B</xref>).</p></sec><sec id="s3-3"><title>Awake mouse fMRI with vibrissa stimulation</title><p>In contrast to a visual sensation, awake mice may flinch due to the sudden physical vibrissa stimulation causing severe motion artifacts during scanning. Prolonged training was needed to reduce motion artifacts during air-puff stimulation as shown in <xref ref-type="video" rid="video2">Video 2</xref> allowing for high-resolution fMRI of awake mice. The activated barrel cortex (BC) and ventroposterior medial nucleus (VPM) were seen related to stimulation of the contralateral whisker pad (time courses in <xref ref-type="fig" rid="fig4">Figure 4B</xref>, <xref ref-type="fig" rid="fig3s3">Figure 3—figure supplement 3</xref>). Brain-wide functional maps also showed activation in the motor cortex and a small portion of the ipsilateral BC. These results demonstrated the importance of distinguishing BOLD activation between external stimulation and voluntary movements while also confirming the feasibility to map brain-wide brain activations in awake behaving mice with 14 T fMRI.</p><fig id="fig4" position="float"><label>Figure 4.</label><caption><title>Vibrissa stimulation-evoked high-resolution functional magnetic resonance imaging (fMRI) of awake mice.</title><p>(<bold>A</bold>) The brain-wide functional maps of awake mice show the strong positive blood oxygen level-dependent (BOLD) activation in the contralateral barrel cortex (BC) and ventral posteromedial nucleus (VPM) and posterior thalamic nucleus (PO). Positive BOLD signals are also detected at the motor cortex (MC) and the ventral retrosplenial area (VRA), as well as at the ipsilateral BC and thalamic nuclei. Negative BOLD signals are detected in supplementary somatosensory areas (SSs) (including nose and mouth) as well as part of the caudoputamen. Highlighted brain regions are statistically generated using a one-way T-test with p&lt;0.0001. (<bold>B</bold>) The averaged time course based on the brain atlas ROIs for VMP, BC, and VRA, demonstrating positive BOLD signal changes upon the 8 s air-puff vibrissa stimulation (8 Hz, 10 ms). Averaged time course of the SSs ROI shows negative BOLD signal changes. Each graph displays the average of 279 sets of 3 stimulation epochs. Shaded regions represent standard error. Red lines represent the 8 s stimulation duration. (<bold>C</bold>) The functional maps are overlain with the brain atlas to highlight the activated vibrissa thalamocortical pathway (VPM→BC) and the VRA in awake mice (N=13 (6F/7M)).</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig4-v1.tif"/></fig></sec><sec id="s3-4"><title>Prediction-related barrel cortical activity to patterned air-puff in awake mice</title><p>An interesting observation from the vibrissa stimulation was the activated VRA. The VRA only showed brief responses to air-puff in contrast to the typical duration of hemodynamic responses observed in the BC and VPM. This presents a good landmark for studying higher-level processing of vibrissa sensation. Voxel-wise cross-correlation analysis was performed based on the VRA-specific fMRI dynamic changes. At a zero time shift (map developed from peak BOLD response), the VRA is strongly correlated with the hippocampus, cingulate cortex, and central thalamic regions (<xref ref-type="fig" rid="fig5">Figure 5A</xref>). Nevertheless, at a –6 s time shift (i.e. 2 s before stimulation onset), stronger correlation was observed at the contralateral BC, indicating anticipation of the repetitive air-puff in the block design (<xref ref-type="fig" rid="fig5">Figure 5A</xref>). To validate that this early BC activation was caused by learned anticipation of the time-fixed repetitive air-puff stimulation, we also analyzed the VRA-specific cross-correlation in a control group using a randomized stimulation paradigm. Although VRA remained strongly coupled with the other association cortices and subcortical regions at the zero time shift, no correlation was observed from the contralateral BC at the –6 s time shift (<xref ref-type="fig" rid="fig5">Figure 5B</xref>). The fMRI time course analysis from the contralateral BC also showed increased BOLD responses before the air-puff in the block design group, but not the randomized control group (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). Quantitative analysis showed a significantly higher BOLD signal 2 s before the air-puff stimulation in the standard block design group when compared with the randomized group (<xref ref-type="fig" rid="fig5">Figure 5D</xref>). It should be noted that VRA responses between the two groups were similar, further confirming the anticipation-related early BC activation to repetitive air-puff stimulation.</p><fig id="fig5" position="float"><label>Figure 5.</label><caption><title>Ventral retrosplenial area (VRA)-based brain-wide correlation maps at different time shifts.</title><p>(<bold>A</bold>) The VRA-based correlation maps at –6 s and 0 s time shifts of awake mice with repetitive stimulation (REP). The strong correlation in the contralateral barrel cortex (BC) is shown in the correlation map at the –6 s time shift (red box). Highlighted brain regions are statistically generated using a one-way T-test with p&lt;0.01. (<bold>B</bold>) The VRA-based correlation maps at –6 s and 0 s time shifts of awake mice with randomized stimulation (RAD). No correlation is detected in the contralateral BC at the –6 s time shift (red box). Highlighted brain regions are statistically generated using a one-way T-test with p&lt;0.01 (<bold>C</bold>) The enlarged images from the –6 s time shift correlation maps of REP and RAD groups, demonstrating the strong correlation patterns located at the contralateral BC only in the REP group. (<bold>D</bold>) The averaged time course from both contralateral BC and VRA of REP and RAD groups, showing that early positive blood oxygen level-dependent (BOLD) signals detected at 2 s prior to the stimulation in contralateral BC of the REP group and no significant difference detected in VRA. Shaded regions represent standard error. ❋ shows significance from two-tail two-way T-test (p&lt;0.05). (<bold>E</bold>) The bar graph presents the mean BOLD signals of contralateral BC at 2 s prior to stimulation time point and peak signals of VRA in REP and RAD groups. The inset is the expanded bar graph to show the significantly higher BOLD signals detected in the contralateral BC at 2 s prior to stimulation in REP group using a two-tail two-way T-test (p&lt;0.015, REP graph displays the average of 930 stimulation epochs, RAD graph displays the average of 240 stimulation epochs). (N=9 (4F/5M)).</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-fig5-v1.tif"/></fig></sec></sec><sec id="s4" sec-type="discussion"><title>Discussion</title><p>In this study, we designed and implemented implantable RF coils for awake mouse fMRI, which also served as a headposts during data acquisition. Our design, based on previously published cable-free (inductive) RF coils (<xref ref-type="bibr" rid="bib17">Chen et al., 2022</xref>), offered an easier pre-scan setup by eliminating the need to localize and secure the pickup coil for inductive coupling optimization. And while this current design showed reduced freedom for animal movement, implanted coils offer more stable sample loading and reduce the B<sub>0</sub> offset when compared to the previous version. This was also true when comparing to conventional RF coils as the motion of the animal would alter the loading and cause B<sub>1</sub> field variability during fMRI scanning.</p><sec id="s4-1"><title>Technical considerations with awake mouse fMRI at 14 T</title><p>A few important factors should be considered to improve data quality using the implanted RF coils described in the present study. The first is animal motion. As this design was used for awake and minimally restrained mice, the animals would eventually move to adjust themselves (scratching, grooming, teeth grinding, etc.) during the scan. This will affect B<sub>0</sub> homogeneity and can cause ghosting if severe enough. This can be minimized through acclimation training which will also reduce unwanted stress. Other studies have animal restraint mechanisms that seek to restrain the body of the animal (<xref ref-type="bibr" rid="bib29">Desai et al., 2011</xref>; <xref ref-type="bibr" rid="bib16">Chen et al., 2020</xref>; <xref ref-type="bibr" rid="bib78">Madularu et al., 2017b</xref>; <xref ref-type="bibr" rid="bib47">Harris et al., 2015</xref>) but have the potential to cause unwanted stress which can affect the desired fMRI signals. Furthermore, B<sub>1</sub> variability was present through motion as well due to the current design of the coil. As the RF circuit chip sits above the animal’s neck, body movement could alter the loading of the circuit, inducing B<sub>1</sub> artifacts through lifting or dropping the body toward or away from the circuit chip. Again, these artifacts can be minimized through proper training and stress reduction which was well accomplished for our study through the design and training method (<xref ref-type="bibr" rid="bib137">Xu et al., 2022</xref>). Here, we see that while animal motion still exists (<xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2</xref>) large struggling movements are minimized after the training method. Still, mice have a thin skull, which leads to the air-tissue interface being a non-negligible factor at ultra-high fields (e.g. 14 T). Therefore, the coil implantation shown here has reduced this source of inhomogeneity (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplements 1</xref> and <xref ref-type="fig" rid="fig2s2">2</xref>) and allowed for a consistent and stable shim. By implanting the coil on the surface of the skull, we can achieve a significantly higher SNR which can be comparable to cryoprobe designs at close distances. Moreso, this is the case with the ‘figure 8’ coil shown in this study which gives a five times increase in SNR over the standard commercially available four array mouse head coil for 9.4 T (both operating at room temperature) (<xref ref-type="fig" rid="fig1">Figure 1</xref>). This improvement allows much higher spatial resolution in awake mouse fMRI, at a two nanoliter voxel volume, compared to contemporary efforts in human brain mapping at sub-millimeter resolution (0.5–0.8 mm isotropic), a difference of two orders of magnitude (<xref ref-type="bibr" rid="bib44">Haenelt et al., 2023</xref>; <xref ref-type="bibr" rid="bib48">Heidemann et al., 2012</xref>; <xref ref-type="bibr" rid="bib82">Margalit et al., 2020</xref>; <xref ref-type="bibr" rid="bib34">Feinberg et al., 2018</xref>).</p></sec><sec id="s4-2"><title>The consideration of stress issues of awake mouse fMRI</title><p>Despite the extensive training procedure of the present work in comparison to the existing awake mouse fMRI studies (training strategies for awake mice fMRI have been reviewed by <xref ref-type="bibr" rid="bib80">Mandino et al., 2024</xref> to show the overall training duration of existing studies), stress remains a confounding factor for the brain functional mapping in head-fixed mice. During animal training, we have measured both pupil dynamic and eye motion features from training sessions, both of which could be considered as potential surrogate of the stress levels of animals. It should be noted that stress may be related to increased frequency of eye blinking or twitching movements in human subjects (<xref ref-type="bibr" rid="bib81">Marcos-Ramiro et al., 2014</xref>; <xref ref-type="bibr" rid="bib43">Haak et al., 2009</xref>; <xref ref-type="bibr" rid="bib28">Del Carretto and Sessam, 2023</xref>). However, the eyeblink of head-fixed mice has been used for behavioral conditioning to investigate motor learning in normal behaving mice (<xref ref-type="bibr" rid="bib49">Heiney et al., 2014</xref>; <xref ref-type="bibr" rid="bib18">Chettih et al., 2011</xref>; <xref ref-type="bibr" rid="bib118">Siegel et al., 2015</xref>). Importantly, head-fixed mouse studies have shown that eye movements are significantly reduced compared to the free-moving mice (<xref ref-type="bibr" rid="bib86">Meyer et al., 2020</xref>). The increased eye movement during the acclimation process would indicate an alleviated stress level of the head-fixed mice in our cases. Meanwhile, stress-related pupillary dilation could dominate the pupil dynamics at the early phase of training (<xref ref-type="bibr" rid="bib142">Zeng et al., 2022</xref>). We have observed a gradually increased pupil dynamic power spectrum at the ultra-slow frequency during Phase 3, presenting the alleviated stress-related pupil dilation but recovered pupil dynamics to other factors, including arousal, locomotion, startles, etc. in normal behaving mice. Nevertheless, a recent study (<xref ref-type="bibr" rid="bib55">Juczewski et al., 2020</xref>) shows that the corticosterone concentration in the blood samples of head-fixed mice is significantly reduced on day 25 following the training but remains higher than in the control mice. Also, the time-dependent changes of stress level during scanning could further confound the functional mapping results if longer than 1 hr. Thus, the impact of stress on brain functional mapping with awake mouse fMRI would need further investigation, of which the stress-related functional changes should not be neglected from the existing studies.</p></sec><sec id="s4-3"><title>Brain-wide functional mapping with visual and vibrissa stimulation</title><p>There are fMRI studies investigating the visual system in both anesthetized and awake mice (<xref ref-type="bibr" rid="bib31">Dinh et al., 2021</xref>; <xref ref-type="bibr" rid="bib142">Zeng et al., 2022</xref>; <xref ref-type="bibr" rid="bib50">Huang et al., 1996</xref>; <xref ref-type="bibr" rid="bib64">Lee et al., 2019</xref>; <xref ref-type="bibr" rid="bib90">Niranjan et al., 2016</xref>; <xref ref-type="bibr" rid="bib76">Lungu et al., 2022</xref>). In contrast to brain activation patterns at the VC, SC, and LGN (<xref ref-type="bibr" rid="bib31">Dinh et al., 2021</xref>), robust ACA activation was also detected for awake mouse fMRI in this study (<xref ref-type="fig" rid="fig3">Figure 3</xref>). Since ACA has been closely involved in pupil dynamics, as well as arousal state regulation (<xref ref-type="bibr" rid="bib32">Ebitz and Platt, 2015</xref>; <xref ref-type="bibr" rid="bib54">Joshi et al., 2016</xref>; <xref ref-type="bibr" rid="bib101">Pfeffer et al., 2022</xref>), the mapping of the ACA in awake mice during visual stimulation provides a meaningful way to validate the conscious state of mice during scanning. Similarly, there are extensive rodent fMRI studies of vibrissa stimulation (<xref ref-type="bibr" rid="bib139">You et al., 2021</xref>; <xref ref-type="bibr" rid="bib131">Van der Knaap et al., 2021</xref>; <xref ref-type="bibr" rid="bib74">Lu et al., 2004</xref>; <xref ref-type="bibr" rid="bib6">Balasco et al., 2022</xref>; <xref ref-type="bibr" rid="bib36">Ferrier et al., 2020</xref>; <xref ref-type="bibr" rid="bib20">Choi et al., 2023</xref>). In contrast to the anesthetized state, this awake mouse fMRI detected not only activated contralateral BC and VPM, but also spread activation in the motor cortex, and small portion of the ipsilateral BC with positive BOLD signals. Although the air-puff stimulation was set and verified to deflect the whiskers of chosen side, videos of the mouse during scanning show that active bilateral whisking could be initiated upon air-puff. This could lead to bilateral activation of the motor cortex and the ipsilateral BC. Furthermore, studies have been performed to understand the transcallosal activity-mediated excitatory/inhibitory circuits by both fMRI and optical imaging (<xref ref-type="bibr" rid="bib17">Chen et al., 2022</xref>; <xref ref-type="bibr" rid="bib117">Shim et al., 2020</xref>; <xref ref-type="bibr" rid="bib37">Fujita et al., 2012</xref>; <xref ref-type="bibr" rid="bib41">Grefkes et al., 2008</xref>; <xref ref-type="bibr" rid="bib68">Lenzi et al., 2007</xref>; <xref ref-type="bibr" rid="bib108">Reddy et al., 2000</xref>). The potential transcallosal mediation of the negative BOLD signal detected in the superficial cortical area near BC will need to be further investigated. Also, these negative BOLD signals were detected across a large brain area, which is consistent with astrocyte-mediated negative BOLD during brain state changes reported in anesthetized rats (<xref ref-type="bibr" rid="bib134">Wang et al., 2018b</xref>) and eye open/close-coupled arousal changes in unanesthetized monkeys (<xref ref-type="bibr" rid="bib13">Chang et al., 2016</xref>). Although astrocytic Ca<sup>2+</sup> transients coincide with positive BOLD responses in the activated cortical areas, which align with the neurovascular coupling mechanism (<xref ref-type="bibr" rid="bib125">Takata et al., 2018</xref>), there is emerging evidence to show that astrocytic Ca<sup>2+</sup> transients are coupled with both positive and negative BOLD responses in anesthetized rats (<xref ref-type="bibr" rid="bib134">Wang et al., 2018b</xref>) and awake mice (<xref ref-type="bibr" rid="bib128">Tong et al., 2024</xref>). An intriguing observation is that cortex-wide negative BOLD signals coupled with the spontaneous astrocytic Ca<sup>2+</sup> transients could co-exist with the positive BOLD signal detected at the activated cortex. Studies have shown that astrocytes are involved in regulating brain state changes (<xref ref-type="bibr" rid="bib105">Poskanzer and Yuste, 2016</xref>), in particular, during locomotion (<xref ref-type="bibr" rid="bib96">Paukert et al., 2014</xref>), and startle responses (<xref ref-type="bibr" rid="bib121">Srinivasan et al., 2015</xref>). These brain state-dependent global negative BOLD responses are also related to the arousal changes of both non-human primates (<xref ref-type="bibr" rid="bib13">Chang et al., 2016</xref>) and human subjects (<xref ref-type="bibr" rid="bib113">Setzer et al., 2022</xref>). The established awake mouse fMRI platform with ultra-high spatial resolution will enable the brain-wide activity mapping of the functional nuclei contributing to the brain state changes of head-fixed awake mice in future studies.</p><p>Interestingly, vibrissa stimulation also led to robust VRA activation in awake mice (<xref ref-type="bibr" rid="bib106">Radwanska et al., 2010</xref>). VRA serves as one of the major nodes of the default mode network across different species (<xref ref-type="bibr" rid="bib75">Lu et al., 2012</xref>; <xref ref-type="bibr" rid="bib3">Andrews-Hanna et al., 2010</xref>; <xref ref-type="bibr" rid="bib132">Vincent et al., 2007</xref>; <xref ref-type="bibr" rid="bib109">Rilling et al., 2007</xref>; <xref ref-type="bibr" rid="bib107">Raichle et al., 2001</xref>). The vibrissa stimulation-evoked VRA activation suggests the higher-level cortical function contribute to vibrissa sensory processing in awake mice.</p></sec><sec id="s4-4"><title>VRA-coupled pre-stimulus BC activation in awake mice as a sign of anticipation</title><p>There are extensive studies investigating brain activation responsible for anticipation with fMRI and electrophysiological recordings (<xref ref-type="bibr" rid="bib145">Zhao et al., 2019</xref>; <xref ref-type="bibr" rid="bib83">Martin et al., 2009</xref>; <xref ref-type="bibr" rid="bib146">Zhao et al., 2022</xref>; <xref ref-type="bibr" rid="bib103">Ploghaus et al., 2003</xref>; <xref ref-type="bibr" rid="bib119">Sirotin and Das, 2009</xref>). In contrast to the reward anticipation or audiovisual anticipation of naturalistic music and movie clips that demand more complex cognitive processing (<xref ref-type="bibr" rid="bib100">Pezzulo et al., 2007</xref>; <xref ref-type="bibr" rid="bib85">McRobert et al., 2011</xref>; <xref ref-type="bibr" rid="bib12">Burton et al., 2009</xref>; <xref ref-type="bibr" rid="bib21">Ciesielski et al., 2012</xref>), the repetitive air-puff stimulation delivered during head-fixed training for fMRI studies could serve as a simple paradigm to process the anticipatory responses in awake mice. Based on cross-correlation analysis with evoked VRA BOLD responses, the strongest correlation with the BC was detected from 6 s lag-time-based correlation maps, showing a positive BOLD signal at a time point 2 s prior to stimulus onset (<xref ref-type="fig" rid="fig5">Figure 5</xref>). This anticipatory BC response was not detected when the air-puff stimulation paradigm was randomized in another group of mice. VRA is known to be involved in prediction (<xref ref-type="bibr" rid="bib120">Smith et al., 2018</xref>; <xref ref-type="bibr" rid="bib87">Miller et al., 2019</xref>; <xref ref-type="bibr" rid="bib5">Auger and Maguire, 2013</xref>) and has been coupled with temporal prediction in rodents (<xref ref-type="bibr" rid="bib87">Miller et al., 2019</xref>; <xref ref-type="bibr" rid="bib136">Wyass and Van Groen, 1992</xref>), as well as navigation efficiency involving spatial reference cues (<xref ref-type="bibr" rid="bib87">Miller et al., 2019</xref>; <xref ref-type="bibr" rid="bib5">Auger and Maguire, 2013</xref>; <xref ref-type="bibr" rid="bib136">Wyass and Van Groen, 1992</xref>). Additionally, external somatosensory cues (e.g. the air-puff or brushing of whiskers) are an important factor when investigating prediction processing (<xref ref-type="bibr" rid="bib126">Taube, 2007</xref>; <xref ref-type="bibr" rid="bib130">Valerio and Taube, 2012</xref>; <xref ref-type="bibr" rid="bib127">Todd et al., 2019</xref>; <xref ref-type="bibr" rid="bib23">Cooper et al., 2001</xref>; <xref ref-type="bibr" rid="bib59">Keene and Bucci, 2021</xref>). Previous work has shown that prediction of external stimulation will cause a hemodynamic response even in the absence of a stimulus (<xref ref-type="bibr" rid="bib119">Sirotin and Das, 2009</xref>; <xref ref-type="bibr" rid="bib141">Yu et al., 2019</xref>). In our study, we show that after continued regularly spaced stimulation, early somatosensory hemodynamic responses begin to have a significant impact seen in the averaged BOLD response time course. These anticipatory hemodynamic responses are a result of the continuous training for mice experiencing months of repetitive stimulation. The increased BOLD signal in the BC before the stimulus onset shows strong cross-correlation to the VRA activation, but VRA activation is not dependent on the pre-stimulus activation in the BC. This can be seen through the comparable VRA BOLD responses between repetitive and randomized air-puff stimulation paradigms (<xref ref-type="fig" rid="fig5">Figure 5C</xref>). This result indicates that VRA response mediates external sensory perception and may serve as a key association cortical area for the processing of the anticipated vibrissa signals but is not solely dependent on the prediction of incoming stimulus.</p></sec></sec></body><back><sec sec-type="additional-information" id="s5"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="COI-statement" id="conf1"><p>No competing interests declared</p></fn><fn fn-type="COI-statement" id="conf2"><p>Cofounder of MRIBOT LLC</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>Conceptualization, Resources, Data curation, Formal analysis, Validation, Investigation, Methodology, Writing – original draft, Project administration, Writing – review and editing</p></fn><fn fn-type="con" id="con2"><p>Conceptualization, Resources, Data curation, Formal analysis, Validation, Investigation, Methodology, Writing – original draft, Project administration, Writing – review and editing</p></fn><fn fn-type="con" id="con3"><p>Data curation, Investigation, Methodology</p></fn><fn fn-type="con" id="con4"><p>Resources, Validation, Methodology</p></fn><fn fn-type="con" id="con5"><p>Software, Formal analysis</p></fn><fn fn-type="con" id="con6"><p>Formal analysis, Methodology</p></fn><fn fn-type="con" id="con7"><p>Resources, Data curation</p></fn><fn fn-type="con" id="con8"><p>Resources, Formal analysis</p></fn><fn fn-type="con" id="con9"><p>Formal analysis</p></fn><fn fn-type="con" id="con10"><p>Resources, Funding acquisition, Writing – review and editing</p></fn><fn fn-type="con" id="con11"><p>Conceptualization, Data curation, Supervision, Funding acquisition, Methodology, Writing – review and editing</p></fn></fn-group><fn-group content-type="ethics-information"><title>Ethics</title><fn fn-type="other"><p>All animal procedures were conducted in accordance with protocols approved by the Massachusetts General Hospital (MGH) Institutional Animal Care and Use Committee (IACUC), and animals were cared for according to the requirements of the National Research Council's Guide for the Care and Use of Laboratory Animals.</p></fn></fn-group></sec><sec sec-type="supplementary-material" id="s6"><title>Additional files</title><supplementary-material id="mdar"><label>MDAR checklist</label><media xlink:href="elife-95528-mdarchecklist1-v1.docx" mimetype="application" mime-subtype="docx"/></supplementary-material></sec><sec sec-type="data-availability" id="s7"><title>Data availability</title><p>Data is available for download from OpenNeuro: Whisker (<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.18112/openneuro.ds005496.v1.0.1">https://doi.org/10.18112/openneuro.ds005496.v1.0.1</ext-link>), Visual (<ext-link ext-link-type="uri" xlink:href="https://doi.org/10.18112/openneuro.ds005497.v1.0.0">https://doi.org/10.18112/openneuro.ds005497.v1.0.0</ext-link>) and Zenodo:SNR Line Profile Data &amp; Data Processing Scripts: (<ext-link ext-link-type="uri" xlink:href="https://zenodo.org/doi/10.5281/zenodo.13821455">https://zenodo.org/doi/10.5281/zenodo.13821455</ext-link>).</p><p>The following datasets were generated:</p><p><element-citation publication-type="data" specific-use="isSupplementedBy" id="dataset1"><person-group person-group-type="author"><name><surname>Hike</surname><given-names>D</given-names></name><name><surname>Liu</surname><given-names>X</given-names></name><name><surname>Xie</surname><given-names>Z</given-names></name><name><surname>Zhang</surname><given-names>B</given-names></name><name><surname>Choi</surname><given-names>S</given-names></name><name><surname>Zhou</surname><given-names>XA</given-names></name><name><surname>Liu</surname><given-names>A</given-names></name><name><surname>Murstein</surname><given-names>A</given-names></name><name><surname>Jiang</surname><given-names>Y</given-names></name><name><surname>Devor</surname><given-names>A</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2024">2024</year><data-title>Whisker Stim</data-title><source>OpenNeuro</source><pub-id pub-id-type="accession" xlink:href="https://openneuro.org/datasets/ds005496/versions/1.0.1">ds005496</pub-id></element-citation></p><p><element-citation publication-type="data" specific-use="isSupplementedBy" id="dataset2"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>X</given-names></name><name><surname>Hike</surname><given-names>D</given-names></name><name><surname>Choi</surname><given-names>S</given-names></name><name><surname>Man</surname><given-names>W</given-names></name><name><surname>Ran</surname><given-names>C</given-names></name><name><surname>Zhou</surname><given-names>XA</given-names></name><name><surname>Jiang</surname><given-names>Y</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2024">2024</year><data-title>Visual Stim</data-title><source>OpenNeuro</source><pub-id pub-id-type="accession" xlink:href="https://openneuro.org/datasets/ds005497/versions/1.0.0">ds005497</pub-id></element-citation></p><p><element-citation publication-type="data" specific-use="isSupplementedBy" id="dataset3"><person-group person-group-type="author"><name><surname>Hike</surname><given-names>D</given-names></name><name><surname>Liu</surname><given-names>X</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2024">2024</year><data-title>Awake Mouse</data-title><source>Zenodo</source><pub-id pub-id-type="doi">10.5281/zenodo.13821456</pub-id></element-citation></p></sec><ack id="ack"><title>Acknowledgements</title><p>The research benefited from funding from the NIH Brain Initiative grants (RF1NS113278, RF1NS124778, R01NS122904, R01NS120594, and R21NS121642), U19 Cooperative Agreement Grant (U19NS123717), S10 instrument grants (S10OD028616 and S10RR025563) to the MGH/Harvard-MIT Program in Health Sciences and Technology Martinos Center, and NSF CBET grant (2123970).</p></ack><ref-list><title>References</title><ref id="bib1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Abe</surname><given-names>Y</given-names></name><name><surname>Kwon</surname><given-names>S</given-names></name><name><surname>Oishi</surname><given-names>M</given-names></name><name><surname>Unekawa</surname><given-names>M</given-names></name><name><surname>Takata</surname><given-names>N</given-names></name><name><surname>Seki</surname><given-names>F</given-names></name><name><surname>Koyama</surname><given-names>R</given-names></name><name><surname>Abe</surname><given-names>M</given-names></name><name><surname>Sakimura</surname><given-names>K</given-names></name><name><surname>Masamoto</surname><given-names>K</given-names></name><name><surname>Tomita</surname><given-names>Y</given-names></name><name><surname>Okano</surname><given-names>H</given-names></name><name><surname>Mushiake</surname><given-names>H</given-names></name><name><surname>Tanaka</surname><given-names>KF</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Optical manipulation of local cerebral blood flow in the deep brain of freely moving mice</article-title><source>Cell Reports</source><volume>36</volume><elocation-id>109427</elocation-id><pub-id pub-id-type="doi">10.1016/j.celrep.2021.109427</pub-id><pub-id pub-id-type="pmid">34320360</pub-id></element-citation></ref><ref id="bib2"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Almeida</surname><given-names>J</given-names></name><name><surname>Severo</surname><given-names>F</given-names></name><name><surname>Nunes</surname><given-names>D</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Impact of the sound of magnetic resonance imaging pulse sequences in awake mice</article-title><source>Journal of Applied Animal Welfare Science</source><volume>25</volume><fpage>75</fpage><lpage>88</lpage><pub-id pub-id-type="doi">10.1080/10888705.2021.1941023</pub-id><pub-id pub-id-type="pmid">34286640</pub-id></element-citation></ref><ref id="bib3"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Andrews-Hanna</surname><given-names>JR</given-names></name><name><surname>Reidler</surname><given-names>JS</given-names></name><name><surname>Sepulcre</surname><given-names>J</given-names></name><name><surname>Poulin</surname><given-names>R</given-names></name><name><surname>Buckner</surname><given-names>RL</given-names></name></person-group><year iso-8601-date="2010">2010</year><article-title>Functional-anatomic fractionation of the brain’s default network</article-title><source>Neuron</source><volume>65</volume><fpage>550</fpage><lpage>562</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2010.02.005</pub-id><pub-id pub-id-type="pmid">20188659</pub-id></element-citation></ref><ref id="bib4"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Arbabi</surname><given-names>A</given-names></name><name><surname>Spencer Noakes</surname><given-names>L</given-names></name><name><surname>Vousden</surname><given-names>D</given-names></name><name><surname>Dazai</surname><given-names>J</given-names></name><name><surname>Spring</surname><given-names>S</given-names></name><name><surname>Botelho</surname><given-names>O</given-names></name><name><surname>Keshavarzian</surname><given-names>T</given-names></name><name><surname>Mattingly</surname><given-names>M</given-names></name><name><surname>Ellegood</surname><given-names>JE</given-names></name><name><surname>Nutter</surname><given-names>LMJ</given-names></name><name><surname>Wissmann</surname><given-names>R</given-names></name><name><surname>Sled</surname><given-names>JG</given-names></name><name><surname>Lerch</surname><given-names>JP</given-names></name><name><surname>Henkelman</surname><given-names>RM</given-names></name><name><surname>Nieman</surname><given-names>BJ</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Multiple-mouse magnetic resonance imaging with cryogenic radiofrequency probes for evaluation of brain development</article-title><source>NeuroImage</source><volume>252</volume><elocation-id>119008</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2022.119008</pub-id><pub-id pub-id-type="pmid">35245675</pub-id></element-citation></ref><ref id="bib5"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Auger</surname><given-names>SD</given-names></name><name><surname>Maguire</surname><given-names>EA</given-names></name></person-group><year iso-8601-date="2013">2013</year><article-title>Assessing the mechanism of response in the retrosplenial cortex of good and poor navigators</article-title><source>Cortex</source><volume>49</volume><fpage>2904</fpage><lpage>2913</lpage><pub-id pub-id-type="doi">10.1016/j.cortex.2013.08.002</pub-id><pub-id pub-id-type="pmid">24012136</pub-id></element-citation></ref><ref id="bib6"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Balasco</surname><given-names>L</given-names></name><name><surname>Pagani</surname><given-names>M</given-names></name><name><surname>Pangrazzi</surname><given-names>L</given-names></name><name><surname>Chelini</surname><given-names>G</given-names></name><name><surname>Ciancone Chama</surname><given-names>AG</given-names></name><name><surname>Shlosman</surname><given-names>E</given-names></name><name><surname>Mattioni</surname><given-names>L</given-names></name><name><surname>Galbusera</surname><given-names>A</given-names></name><name><surname>Iurilli</surname><given-names>G</given-names></name><name><surname>Provenzano</surname><given-names>G</given-names></name><name><surname>Gozzi</surname><given-names>A</given-names></name><name><surname>Bozzi</surname><given-names>Y</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Abnormal whisker-dependent behaviors and altered cortico-hippocampal connectivity in shank3b-/- mice</article-title><source>Cerebral Cortex</source><volume>32</volume><fpage>3042</fpage><lpage>3056</lpage><pub-id pub-id-type="doi">10.1093/cercor/bhab399</pub-id><pub-id pub-id-type="pmid">34791077</pub-id></element-citation></ref><ref id="bib7"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Baltes</surname><given-names>C</given-names></name><name><surname>Radzwill</surname><given-names>N</given-names></name><name><surname>Bosshard</surname><given-names>S</given-names></name><name><surname>Marek</surname><given-names>D</given-names></name><name><surname>Rudin</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Micro MRI of the mouse brain using a novel 400 MHz cryogenic quadrature RF probe</article-title><source>NMR in Biomedicine</source><volume>22</volume><fpage>834</fpage><lpage>842</lpage><pub-id pub-id-type="doi">10.1002/nbm.1396</pub-id><pub-id pub-id-type="pmid">19536757</pub-id></element-citation></ref><ref id="bib8"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bandettini</surname><given-names>PA</given-names></name><name><surname>Wong</surname><given-names>EC</given-names></name><name><surname>Hinks</surname><given-names>RS</given-names></name><name><surname>Tikofsky</surname><given-names>RS</given-names></name><name><surname>Hyde</surname><given-names>JS</given-names></name></person-group><year iso-8601-date="1992">1992</year><article-title>Time course EPI of human brain function during task activation</article-title><source>Magnetic Resonance in Medicine</source><volume>25</volume><fpage>390</fpage><lpage>397</lpage><pub-id pub-id-type="doi">10.1002/mrm.1910250220</pub-id><pub-id pub-id-type="pmid">1614324</pub-id></element-citation></ref><ref id="bib9"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Becq</surname><given-names>GJPC</given-names></name><name><surname>Barbier</surname><given-names>EL</given-names></name><name><surname>Achard</surname><given-names>S</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Brain networks of rats under anesthesia using resting-state fMRI: comparison with dead rats, random noise and generative models of networks</article-title><source>Journal of Neural Engineering</source><volume>17</volume><elocation-id>045012</elocation-id><pub-id pub-id-type="doi">10.1088/1741-2552/ab9fec</pub-id><pub-id pub-id-type="pmid">32580176</pub-id></element-citation></ref><ref id="bib10"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bukhari</surname><given-names>Q</given-names></name><name><surname>Schroeter</surname><given-names>A</given-names></name><name><surname>Cole</surname><given-names>DM</given-names></name><name><surname>Rudin</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>Resting State fMRI in mice reveals anesthesia specific signatures of brain functional networks and their interactions</article-title><source>Frontiers in Neural Circuits</source><volume>11</volume><elocation-id>5</elocation-id><pub-id pub-id-type="doi">10.3389/fncir.2017.00005</pub-id><pub-id pub-id-type="pmid">28217085</pub-id></element-citation></ref><ref id="bib11"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bukhari</surname><given-names>Q</given-names></name><name><surname>Schroeter</surname><given-names>A</given-names></name><name><surname>Rudin</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>Increasing isoflurane dose reduces homotopic correlation and functional segregation of brain networks in mice as revealed by resting-state fMRI</article-title><source>Scientific Reports</source><volume>8</volume><elocation-id>10591</elocation-id><pub-id pub-id-type="doi">10.1038/s41598-018-28766-3</pub-id><pub-id pub-id-type="pmid">30002419</pub-id></element-citation></ref><ref id="bib12"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burton</surname><given-names>BG</given-names></name><name><surname>Hok</surname><given-names>V</given-names></name><name><surname>Save</surname><given-names>E</given-names></name><name><surname>Poucet</surname><given-names>B</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Lesion of the ventral and intermediate hippocampus abolishes anticipatory activity in the medial prefrontal cortex of the rat</article-title><source>Behavioural Brain Research</source><volume>199</volume><fpage>222</fpage><lpage>234</lpage><pub-id pub-id-type="doi">10.1016/j.bbr.2008.11.045</pub-id><pub-id pub-id-type="pmid">19103227</pub-id></element-citation></ref><ref id="bib13"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chang</surname><given-names>C</given-names></name><name><surname>Leopold</surname><given-names>DA</given-names></name><name><surname>Schölvinck</surname><given-names>ML</given-names></name><name><surname>Mandelkow</surname><given-names>H</given-names></name><name><surname>Picchioni</surname><given-names>D</given-names></name><name><surname>Liu</surname><given-names>X</given-names></name><name><surname>Ye</surname><given-names>FQ</given-names></name><name><surname>Turchi</surname><given-names>JN</given-names></name><name><surname>Duyn</surname><given-names>JH</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Tracking brain arousal fluctuations with fMRI</article-title><source>PNAS</source><volume>113</volume><fpage>4518</fpage><lpage>4523</lpage><pub-id pub-id-type="doi">10.1073/pnas.1520613113</pub-id><pub-id pub-id-type="pmid">27051064</pub-id></element-citation></ref><ref id="bib14"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>Y</given-names></name><name><surname>Pais-Roldan</surname><given-names>P</given-names></name><name><surname>Chen</surname><given-names>X</given-names></name><name><surname>Frosz</surname><given-names>MH</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2019">2019a</year><article-title>MRI-guided robotic arm drives optogenetic fMRI with concurrent Ca2+ recording</article-title><source>Nature Communications</source><volume>10</volume><fpage>1</fpage><lpage>11</lpage><pub-id pub-id-type="doi">10.1038/s41467-019-10450-3</pub-id></element-citation></ref><ref id="bib15"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>X</given-names></name><name><surname>Sobczak</surname><given-names>F</given-names></name><name><surname>Chen</surname><given-names>Y</given-names></name><name><surname>Jiang</surname><given-names>Y</given-names></name><name><surname>Qian</surname><given-names>C</given-names></name><name><surname>Lu</surname><given-names>Z</given-names></name><name><surname>Ayata</surname><given-names>C</given-names></name><name><surname>Logothetis</surname><given-names>NK</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2019">2019b</year><article-title>Mapping optogenetically-driven single-vessel fMRI with concurrent neuronal calcium recordings in the rat hippocampus</article-title><source>Nature Communications</source><volume>10</volume><elocation-id>5239</elocation-id><pub-id pub-id-type="doi">10.1038/s41467-019-12850-x</pub-id><pub-id pub-id-type="pmid">31748553</pub-id></element-citation></ref><ref id="bib16"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>X</given-names></name><name><surname>Tong</surname><given-names>C</given-names></name><name><surname>Han</surname><given-names>Z</given-names></name><name><surname>Zhang</surname><given-names>K</given-names></name><name><surname>Bo</surname><given-names>B</given-names></name><name><surname>Feng</surname><given-names>Y</given-names></name><name><surname>Liang</surname><given-names>Z</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Sensory evoked fMRI paradigms in awake mice</article-title><source>NeuroImage</source><volume>204</volume><elocation-id>116242</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2019.116242</pub-id><pub-id pub-id-type="pmid">31586674</pub-id></element-citation></ref><ref id="bib17"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname><given-names>Y</given-names></name><name><surname>Wang</surname><given-names>Q</given-names></name><name><surname>Choi</surname><given-names>S</given-names></name><name><surname>Zeng</surname><given-names>H</given-names></name><name><surname>Takahashi</surname><given-names>K</given-names></name><name><surname>Qian</surname><given-names>C</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Focal fMRI signal enhancement with implantable inductively coupled detectors</article-title><source>NeuroImage</source><volume>247</volume><elocation-id>118793</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2021.118793</pub-id><pub-id pub-id-type="pmid">34896291</pub-id></element-citation></ref><ref id="bib18"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chettih</surname><given-names>SN</given-names></name><name><surname>McDougle</surname><given-names>SD</given-names></name><name><surname>Ruffolo</surname><given-names>LI</given-names></name><name><surname>Medina</surname><given-names>JF</given-names></name></person-group><year iso-8601-date="2011">2011</year><article-title>Adaptive timing of motor output in the mouse: the role of movement oscillations in eyelid conditioning</article-title><source>Frontiers in Integrative Neuroscience</source><volume>5</volume><elocation-id>72</elocation-id><pub-id pub-id-type="doi">10.3389/fnint.2011.00072</pub-id><pub-id pub-id-type="pmid">22144951</pub-id></element-citation></ref><ref id="bib19"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chiba</surname><given-names>S</given-names></name><name><surname>Numakawa</surname><given-names>T</given-names></name><name><surname>Ninomiya</surname><given-names>M</given-names></name><name><surname>Richards</surname><given-names>MC</given-names></name><name><surname>Wakabayashi</surname><given-names>C</given-names></name><name><surname>Kunugi</surname><given-names>H</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Chronic restraint stress causes anxiety- and depression-like behaviors, downregulates glucocorticoid receptor expression, and attenuates glutamate release induced by brain-derived neurotrophic factor in the prefrontal cortex</article-title><source>Progress in Neuro-Psychopharmacology &amp; Biological Psychiatry</source><volume>39</volume><fpage>112</fpage><lpage>119</lpage><pub-id pub-id-type="doi">10.1016/j.pnpbp.2012.05.018</pub-id><pub-id pub-id-type="pmid">22664354</pub-id></element-citation></ref><ref id="bib20"><element-citation publication-type="preprint"><person-group person-group-type="author"><name><surname>Choi</surname><given-names>SH</given-names></name><name><surname>Im</surname><given-names>GH</given-names></name><name><surname>Choi</surname><given-names>S</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name><name><surname>Bandettini</surname><given-names>PA</given-names></name><name><surname>Menon</surname><given-names>RS</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2023">2023</year><article-title>No replication of direct neuronal activity-related (DIANA) fMRI in anesthetized mice</article-title><source>bioRxiv</source><pub-id pub-id-type="doi">10.1101/2023.05.26.542419</pub-id></element-citation></ref><ref id="bib21"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ciesielski</surname><given-names>KT</given-names></name><name><surname>Rauch</surname><given-names>SL</given-names></name><name><surname>Ahlfors</surname><given-names>SP</given-names></name><name><surname>Vangel</surname><given-names>ME</given-names></name><name><surname>Wilhelm</surname><given-names>S</given-names></name><name><surname>Rosen</surname><given-names>BR</given-names></name><name><surname>Hämäläinen</surname><given-names>MS</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Role of medial cortical networks for anticipatory processing in obsessive-compulsive disorder</article-title><source>Human Brain Mapping</source><volume>33</volume><fpage>2125</fpage><lpage>2134</lpage><pub-id pub-id-type="doi">10.1002/hbm.21341</pub-id><pub-id pub-id-type="pmid">21882299</pub-id></element-citation></ref><ref id="bib22"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Conzen</surname><given-names>PF</given-names></name><name><surname>Vollmar</surname><given-names>B</given-names></name><name><surname>Habazettl</surname><given-names>H</given-names></name><name><surname>Frink</surname><given-names>EJ</given-names></name><name><surname>Peter</surname><given-names>K</given-names></name><name><surname>Messmer</surname><given-names>K</given-names></name></person-group><year iso-8601-date="1992">1992</year><article-title>Systemic and regional hemodynamics of isoflurane and sevoflurane in rats</article-title><source>Anesthesia and Analgesia</source><volume>74</volume><fpage>79</fpage><lpage>88</lpage><pub-id pub-id-type="doi">10.1213/00000539-199201000-00014</pub-id><pub-id pub-id-type="pmid">1734802</pub-id></element-citation></ref><ref id="bib23"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cooper</surname><given-names>BG</given-names></name><name><surname>Manka</surname><given-names>TF</given-names></name><name><surname>Mizumori</surname><given-names>SJY</given-names></name></person-group><year iso-8601-date="2001">2001</year><article-title>Finding your way in the dark: The retrosplenial cortex contributes to spatial memory and navigation without visual cues</article-title><source>Behavioral Neuroscience</source><volume>115</volume><fpage>1012</fpage><lpage>1028</lpage><pub-id pub-id-type="doi">10.1037//0735-7044.115.5.1012</pub-id></element-citation></ref><ref id="bib24"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cover</surname><given-names>CG</given-names></name><name><surname>Kesner</surname><given-names>AJ</given-names></name><name><surname>Ukani</surname><given-names>S</given-names></name><name><surname>Stein</surname><given-names>EA</given-names></name><name><surname>Ikemoto</surname><given-names>S</given-names></name><name><surname>Yang</surname><given-names>Y</given-names></name><name><surname>Lu</surname><given-names>H</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Whole brain dynamics during optogenetic self-stimulation of the medial prefrontal cortex in mice</article-title><source>Communications Biology</source><volume>4</volume><elocation-id>66</elocation-id><pub-id pub-id-type="doi">10.1038/s42003-020-01612-x</pub-id><pub-id pub-id-type="pmid">33446857</pub-id></element-citation></ref><ref id="bib25"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cox</surname><given-names>RW</given-names></name></person-group><year iso-8601-date="1996">1996</year><article-title>AFNI: software for analysis and visualization of functional magnetic resonance neuroimages</article-title><source>Computers and Biomedical Research, an International Journal</source><volume>29</volume><fpage>162</fpage><lpage>173</lpage><pub-id pub-id-type="doi">10.1006/cbmr.1996.0014</pub-id><pub-id pub-id-type="pmid">8812068</pub-id></element-citation></ref><ref id="bib26"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cox</surname><given-names>RW</given-names></name><name><surname>Hyde</surname><given-names>JS</given-names></name></person-group><year iso-8601-date="1997">1997</year><article-title>Software tools for analysis and visualization of fMRI data</article-title><source>NMR in Biomedicine</source><volume>10</volume><fpage>171</fpage><lpage>178</lpage><pub-id pub-id-type="doi">10.1002/(sici)1099-1492(199706/08)10:4/5&lt;171::aid-nbm453&gt;3.0.co;2-l</pub-id><pub-id pub-id-type="pmid">9430344</pub-id></element-citation></ref><ref id="bib27"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Crawford</surname><given-names>MW</given-names></name><name><surname>Lerman</surname><given-names>J</given-names></name><name><surname>Saldivia</surname><given-names>V</given-names></name><name><surname>Carmichael</surname><given-names>FJ</given-names></name></person-group><year iso-8601-date="1992">1992</year><article-title>Hemodynamic and organ blood flow responses to halothane and sevoflurane anesthesia during spontaneous ventilation</article-title><source>Anesthesia and Analgesia</source><volume>75</volume><fpage>1000</fpage><lpage>1006</lpage><pub-id pub-id-type="doi">10.1213/00000539-199212000-00021</pub-id><pub-id pub-id-type="pmid">1443679</pub-id></element-citation></ref><ref id="bib28"><element-citation publication-type="book"><person-group person-group-type="author"><name><surname>Del Carretto</surname><given-names>E</given-names></name><name><surname>Sessam</surname><given-names>E</given-names></name></person-group><year iso-8601-date="2023">2023</year><source>Exploring the Impact of Stress and Cognitive Workload on Eye Movements: A Preliminary Study</source><publisher-name>Politecnico di Torino</publisher-name></element-citation></ref><ref id="bib29"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Desai</surname><given-names>M</given-names></name><name><surname>Kahn</surname><given-names>I</given-names></name><name><surname>Knoblich</surname><given-names>U</given-names></name><name><surname>Bernstein</surname><given-names>J</given-names></name><name><surname>Atallah</surname><given-names>H</given-names></name><name><surname>Yang</surname><given-names>A</given-names></name><name><surname>Kopell</surname><given-names>N</given-names></name><name><surname>Buckner</surname><given-names>RL</given-names></name><name><surname>Graybiel</surname><given-names>AM</given-names></name><name><surname>Moore</surname><given-names>CI</given-names></name><name><surname>Boyden</surname><given-names>ES</given-names></name></person-group><year iso-8601-date="2011">2011</year><article-title>Mapping brain networks in awake mice using combined optical neural control and fMRI</article-title><source>Journal of Neurophysiology</source><volume>105</volume><fpage>1393</fpage><lpage>1405</lpage><pub-id pub-id-type="doi">10.1152/jn.00828.2010</pub-id><pub-id pub-id-type="pmid">21160013</pub-id></element-citation></ref><ref id="bib30"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Desjardins</surname><given-names>M</given-names></name><name><surname>Kılıç</surname><given-names>K</given-names></name><name><surname>Thunemann</surname><given-names>M</given-names></name><name><surname>Mateo</surname><given-names>C</given-names></name><name><surname>Holland</surname><given-names>D</given-names></name><name><surname>Ferri</surname><given-names>CGL</given-names></name><name><surname>Cremonesi</surname><given-names>JA</given-names></name><name><surname>Li</surname><given-names>B</given-names></name><name><surname>Cheng</surname><given-names>Q</given-names></name><name><surname>Weldy</surname><given-names>KL</given-names></name><name><surname>Saisan</surname><given-names>PA</given-names></name><name><surname>Kleinfeld</surname><given-names>D</given-names></name><name><surname>Komiyama</surname><given-names>T</given-names></name><name><surname>Liu</surname><given-names>TT</given-names></name><name><surname>Bussell</surname><given-names>R</given-names></name><name><surname>Wong</surname><given-names>EC</given-names></name><name><surname>Scadeng</surname><given-names>M</given-names></name><name><surname>Dunn</surname><given-names>AK</given-names></name><name><surname>Boas</surname><given-names>DA</given-names></name><name><surname>Sakadžić</surname><given-names>S</given-names></name><name><surname>Mandeville</surname><given-names>JB</given-names></name><name><surname>Buxton</surname><given-names>RB</given-names></name><name><surname>Dale</surname><given-names>AM</given-names></name><name><surname>Devor</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Awake mouse imaging: from two-photon microscopy to blood oxygen level-dependent functional magnetic resonance imaging</article-title><source>Biological Psychiatry</source><volume>4</volume><fpage>533</fpage><lpage>542</lpage><pub-id pub-id-type="doi">10.1016/j.bpsc.2018.12.002</pub-id><pub-id pub-id-type="pmid">30691968</pub-id></element-citation></ref><ref id="bib31"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dinh</surname><given-names>TNA</given-names></name><name><surname>Jung</surname><given-names>WB</given-names></name><name><surname>Shim</surname><given-names>HJ</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Characteristics of fMRI responses to visual stimulation in anesthetized vs. awake mice</article-title><source>NeuroImage</source><volume>226</volume><elocation-id>117542</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2020.117542</pub-id><pub-id pub-id-type="pmid">33186719</pub-id></element-citation></ref><ref id="bib32"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ebitz</surname><given-names>RB</given-names></name><name><surname>Platt</surname><given-names>ML</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Neuronal activity in primate dorsal anterior cingulate cortex signals task conflict and predicts adjustments in pupil-linked arousal</article-title><source>Neuron</source><volume>85</volume><fpage>628</fpage><lpage>640</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2014.12.053</pub-id><pub-id pub-id-type="pmid">25654259</pub-id></element-citation></ref><ref id="bib33"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Farmer</surname><given-names>THR</given-names></name><name><surname>Cofer</surname><given-names>GP</given-names></name><name><surname>Johnson</surname><given-names>GA</given-names></name></person-group><year iso-8601-date="1990">1990</year><article-title>Maximizing contrast to noise with inductively coupled implanted coils</article-title><source>Investigative Radiology</source><volume>25</volume><fpage>552</fpage><lpage>558</lpage><pub-id pub-id-type="doi">10.1097/00004424-199005000-00013</pub-id><pub-id pub-id-type="pmid">2345087</pub-id></element-citation></ref><ref id="bib34"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Feinberg</surname><given-names>DA</given-names></name><name><surname>Vu</surname><given-names>AT</given-names></name><name><surname>Beckett</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>Pushing the limits of ultra-high resolution human brain imaging with SMS-EPI demonstrated for columnar level fMRI</article-title><source>NeuroImage</source><volume>164</volume><fpage>155</fpage><lpage>163</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2017.02.020</pub-id><pub-id pub-id-type="pmid">28213116</pub-id></element-citation></ref><ref id="bib35"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ferenczi</surname><given-names>EA</given-names></name><name><surname>Zalocusky</surname><given-names>KA</given-names></name><name><surname>Liston</surname><given-names>C</given-names></name><name><surname>Grosenick</surname><given-names>L</given-names></name><name><surname>Warden</surname><given-names>MR</given-names></name><name><surname>Amatya</surname><given-names>D</given-names></name><name><surname>Katovich</surname><given-names>K</given-names></name><name><surname>Mehta</surname><given-names>H</given-names></name><name><surname>Patenaude</surname><given-names>B</given-names></name><name><surname>Ramakrishnan</surname><given-names>C</given-names></name><name><surname>Kalanithi</surname><given-names>P</given-names></name><name><surname>Etkin</surname><given-names>A</given-names></name><name><surname>Knutson</surname><given-names>B</given-names></name><name><surname>Glover</surname><given-names>GH</given-names></name><name><surname>Deisseroth</surname><given-names>K</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Prefrontal cortical regulation of brainwide circuit dynamics and reward-related behavior</article-title><source>Science</source><volume>351</volume><elocation-id>aac9698</elocation-id><pub-id pub-id-type="doi">10.1126/science.aac9698</pub-id><pub-id pub-id-type="pmid">26722001</pub-id></element-citation></ref><ref id="bib36"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ferrier</surname><given-names>J</given-names></name><name><surname>Tiran</surname><given-names>E</given-names></name><name><surname>Deffieux</surname><given-names>T</given-names></name><name><surname>Tanter</surname><given-names>M</given-names></name><name><surname>Lenkei</surname><given-names>Z</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Functional imaging evidence for task-induced deactivation and disconnection of a major default mode network hub in the mouse brain</article-title><source>PNAS</source><volume>117</volume><fpage>15270</fpage><lpage>15280</lpage><pub-id pub-id-type="doi">10.1073/pnas.1920475117</pub-id></element-citation></ref><ref id="bib37"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Fujita</surname><given-names>S</given-names></name><name><surname>Kitayama</surname><given-names>T</given-names></name><name><surname>Mizoguchi</surname><given-names>N</given-names></name><name><surname>Oi</surname><given-names>Y</given-names></name><name><surname>Koshikawa</surname><given-names>N</given-names></name><name><surname>Kobayashi</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Spatiotemporal profiles of transcallosal connections in rat insular cortex revealed by in vivo optical imaging</article-title><source>Neuroscience</source><volume>206</volume><fpage>201</fpage><lpage>211</lpage><pub-id pub-id-type="doi">10.1016/j.neuroscience.2012.01.014</pub-id><pub-id pub-id-type="pmid">22285884</pub-id></element-citation></ref><ref id="bib38"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gargiulo</surname><given-names>S</given-names></name><name><surname>Greco</surname><given-names>A</given-names></name><name><surname>Gramanzini</surname><given-names>M</given-names></name><name><surname>Esposito</surname><given-names>S</given-names></name><name><surname>Affuso</surname><given-names>A</given-names></name><name><surname>Brunetti</surname><given-names>A</given-names></name><name><surname>Vesce</surname><given-names>G</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Mice anesthesia, analgesia, and care, Part II: anesthetic considerations in preclinical imaging studies</article-title><source>ILAR Journal</source><volume>53</volume><fpage>E70</fpage><lpage>E81</lpage><pub-id pub-id-type="doi">10.1093/ilar.53.1.70</pub-id><pub-id pub-id-type="pmid">23382272</pub-id></element-citation></ref><ref id="bib39"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Giorgi</surname><given-names>A</given-names></name><name><surname>Migliarini</surname><given-names>S</given-names></name><name><surname>Galbusera</surname><given-names>A</given-names></name><name><surname>Maddaloni</surname><given-names>G</given-names></name><name><surname>Mereu</surname><given-names>M</given-names></name><name><surname>Margiani</surname><given-names>G</given-names></name><name><surname>Gritti</surname><given-names>M</given-names></name><name><surname>Landi</surname><given-names>S</given-names></name><name><surname>Trovato</surname><given-names>F</given-names></name><name><surname>Bertozzi</surname><given-names>SM</given-names></name><name><surname>Armirotti</surname><given-names>A</given-names></name><name><surname>Ratto</surname><given-names>GM</given-names></name><name><surname>De Luca</surname><given-names>MA</given-names></name><name><surname>Tonini</surname><given-names>R</given-names></name><name><surname>Gozzi</surname><given-names>A</given-names></name><name><surname>Pasqualetti</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>Brain-wide mapping of endogenous serotonergic transmission via chemogenetic fMRI</article-title><source>Cell Reports</source><volume>21</volume><fpage>910</fpage><lpage>918</lpage><pub-id pub-id-type="doi">10.1016/j.celrep.2017.09.087</pub-id></element-citation></ref><ref id="bib40"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Grandjean</surname><given-names>J</given-names></name><name><surname>Schroeter</surname><given-names>A</given-names></name><name><surname>Batata</surname><given-names>I</given-names></name><name><surname>Rudin</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Optimization of anesthesia protocol for resting-state fMRI in mice based on differential effects of anesthetics on functional connectivity patterns</article-title><source>NeuroImage</source><volume>102 Pt 2</volume><fpage>838</fpage><lpage>847</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2014.08.043</pub-id><pub-id pub-id-type="pmid">25175535</pub-id></element-citation></ref><ref id="bib41"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Grefkes</surname><given-names>C</given-names></name><name><surname>Eickhoff</surname><given-names>SB</given-names></name><name><surname>Nowak</surname><given-names>DA</given-names></name><name><surname>Dafotakis</surname><given-names>M</given-names></name><name><surname>Fink</surname><given-names>GR</given-names></name></person-group><year iso-8601-date="2008">2008</year><article-title>Dynamic intra- and interhemispheric interactions during unilateral and bilateral hand movements assessed with fMRI and DCM</article-title><source>NeuroImage</source><volume>41</volume><fpage>1382</fpage><lpage>1394</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2008.03.048</pub-id><pub-id pub-id-type="pmid">18486490</pub-id></element-citation></ref><ref id="bib42"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gutierrez-Barragan</surname><given-names>D</given-names></name><name><surname>Singh</surname><given-names>NA</given-names></name><name><surname>Alvino</surname><given-names>FG</given-names></name><name><surname>Coletta</surname><given-names>L</given-names></name><name><surname>Rocchi</surname><given-names>F</given-names></name><name><surname>De Guzman</surname><given-names>E</given-names></name><name><surname>Galbusera</surname><given-names>A</given-names></name><name><surname>Uboldi</surname><given-names>M</given-names></name><name><surname>Panzeri</surname><given-names>S</given-names></name><name><surname>Gozzi</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Unique spatiotemporal fMRI dynamics in the awake mouse brain</article-title><source>Current Biology</source><volume>32</volume><fpage>631</fpage><lpage>644</lpage><pub-id pub-id-type="doi">10.1016/j.cub.2021.12.015</pub-id><pub-id pub-id-type="pmid">34998465</pub-id></element-citation></ref><ref id="bib43"><element-citation publication-type="confproc"><person-group person-group-type="author"><name><surname>Haak</surname><given-names>M</given-names></name><name><surname>Bos</surname><given-names>S</given-names></name><name><surname>Panic</surname><given-names>S</given-names></name><name><surname>Rothkrantz</surname><given-names>LJM</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Detecting stress using eye blinks and brain activity from EEG signals</article-title><conf-name>Proceeding of the 1st Driver Car Interaction and Interface (DCII 2008)</conf-name><fpage>35</fpage><lpage>60</lpage></element-citation></ref><ref id="bib44"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Haenelt</surname><given-names>D</given-names></name><name><surname>Trampel</surname><given-names>R</given-names></name><name><surname>Nasr</surname><given-names>S</given-names></name><name><surname>Polimeni</surname><given-names>JR</given-names></name><name><surname>Tootell</surname><given-names>RBH</given-names></name><name><surname>Sereno</surname><given-names>MI</given-names></name><name><surname>Pine</surname><given-names>KJ</given-names></name><name><surname>Edwards</surname><given-names>LJ</given-names></name><name><surname>Helbling</surname><given-names>S</given-names></name><name><surname>Weiskopf</surname><given-names>N</given-names></name></person-group><year iso-8601-date="2023">2023</year><article-title>High-resolution quantitative and functional MRI indicate lower myelination of thin and thick stripes in human secondary visual cortex</article-title><source>eLife</source><volume>12</volume><elocation-id>e78756</elocation-id><pub-id pub-id-type="doi">10.7554/eLife.78756</pub-id><pub-id pub-id-type="pmid">36888685</pub-id></element-citation></ref><ref id="bib45"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hamada</surname><given-names>HT</given-names></name></person-group><year iso-8601-date="2024">2024</year><article-title>Optogenetic activation of dorsal raphe serotonin neurons induces a brain-wide response in reward network</article-title><source>Nature Communications</source><volume>15</volume><elocation-id>4152</elocation-id><pub-id pub-id-type="doi">10.1038/s41467-024-48489-6</pub-id></element-citation></ref><ref id="bib46"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Han</surname><given-names>Z</given-names></name><name><surname>Chen</surname><given-names>W</given-names></name><name><surname>Chen</surname><given-names>X</given-names></name><name><surname>Zhang</surname><given-names>K</given-names></name><name><surname>Tong</surname><given-names>C</given-names></name><name><surname>Zhang</surname><given-names>X</given-names></name><name><surname>Li</surname><given-names>CT</given-names></name><name><surname>Liang</surname><given-names>Z</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Awake and behaving mouse fMRI during Go/No-Go task</article-title><source>NeuroImage</source><volume>188</volume><fpage>733</fpage><lpage>742</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2019.01.002</pub-id><pub-id pub-id-type="pmid">30611875</pub-id></element-citation></ref><ref id="bib47"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Harris</surname><given-names>AP</given-names></name><name><surname>Lennen</surname><given-names>RJ</given-names></name><name><surname>Marshall</surname><given-names>I</given-names></name><name><surname>Jansen</surname><given-names>MA</given-names></name><name><surname>Pernet</surname><given-names>CR</given-names></name><name><surname>Brydges</surname><given-names>NM</given-names></name><name><surname>Duguid</surname><given-names>IC</given-names></name><name><surname>Holmes</surname><given-names>MC</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Imaging learned fear circuitry in awake mice using fMRI</article-title><source>The European Journal of Neuroscience</source><volume>42</volume><fpage>2125</fpage><lpage>2134</lpage><pub-id pub-id-type="doi">10.1111/ejn.12939</pub-id><pub-id pub-id-type="pmid">25943794</pub-id></element-citation></ref><ref id="bib48"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Heidemann</surname><given-names>RM</given-names></name><name><surname>Ivanov</surname><given-names>D</given-names></name><name><surname>Trampel</surname><given-names>R</given-names></name><name><surname>Fasano</surname><given-names>F</given-names></name><name><surname>Meyer</surname><given-names>H</given-names></name><name><surname>Pfeuffer</surname><given-names>J</given-names></name><name><surname>Turner</surname><given-names>R</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Isotropic submillimeter fMRI in the human brain at 7 T: combining reduced field-of-view imaging and partially parallel acquisitions</article-title><source>Magnetic Resonance in Medicine</source><volume>68</volume><fpage>1506</fpage><lpage>1516</lpage><pub-id pub-id-type="doi">10.1002/mrm.24156</pub-id><pub-id pub-id-type="pmid">22231859</pub-id></element-citation></ref><ref id="bib49"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Heiney</surname><given-names>SA</given-names></name><name><surname>Wohl</surname><given-names>MP</given-names></name><name><surname>Chettih</surname><given-names>SN</given-names></name><name><surname>Ruffolo</surname><given-names>LI</given-names></name><name><surname>Medina</surname><given-names>JF</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Cerebellar-dependent expression of motor learning during eyeblink conditioning in head-fixed mice</article-title><source>The Journal of Neuroscience</source><volume>34</volume><fpage>14845</fpage><lpage>14853</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.2820-14.2014</pub-id><pub-id pub-id-type="pmid">25378152</pub-id></element-citation></ref><ref id="bib50"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname><given-names>W</given-names></name><name><surname>Plyka</surname><given-names>I</given-names></name><name><surname>Li</surname><given-names>H</given-names></name><name><surname>Eisenstein</surname><given-names>EM</given-names></name><name><surname>Volkow</surname><given-names>ND</given-names></name><name><surname>Springer</surname><given-names>CS</given-names><suffix>Jr</suffix></name></person-group><year iso-8601-date="1996">1996</year><article-title>Magnetic resonance imaging (MRI) detection of the murine brain response to light: temporal differentiation and negative functional MRI changes</article-title><source>PNAS</source><volume>93</volume><fpage>6037</fpage><lpage>6042</lpage><pub-id pub-id-type="doi">10.1073/pnas.93.12.6037</pub-id></element-citation></ref><ref id="bib51"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ioanas</surname><given-names>H-I</given-names></name><name><surname>Schlegel</surname><given-names>F</given-names></name><name><surname>Skachokova</surname><given-names>Z</given-names></name><name><surname>Schroeter</surname><given-names>A</given-names></name><name><surname>Husak</surname><given-names>T</given-names></name><name><surname>Rudin</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Hybrid fiber optic-fMRI for multimodal cell-specific recording and manipulation of neural activity in rodents</article-title><source>Neurophotonics</source><volume>9</volume><elocation-id>032206</elocation-id><pub-id pub-id-type="doi">10.1117/1.NPh.9.3.032206</pub-id><pub-id pub-id-type="pmid">35355657</pub-id></element-citation></ref><ref id="bib52"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Janke</surname><given-names>AL</given-names></name><name><surname>Ullmann</surname><given-names>JFP</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Robust methods to create ex vivo minimum deformation atlases for brain mapping</article-title><source>Methods</source><volume>73</volume><fpage>18</fpage><lpage>26</lpage><pub-id pub-id-type="doi">10.1016/j.ymeth.2015.01.005</pub-id><pub-id pub-id-type="pmid">25620005</pub-id></element-citation></ref><ref id="bib53"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jonckers</surname><given-names>E</given-names></name><name><surname>Delgado y Palacios</surname><given-names>R</given-names></name><name><surname>Shah</surname><given-names>D</given-names></name><name><surname>Guglielmetti</surname><given-names>C</given-names></name><name><surname>Verhoye</surname><given-names>M</given-names></name><name><surname>Van der Linden</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Different anesthesia regimes modulate the functional connectivity outcome in mice</article-title><source>Magnetic Resonance in Medicine</source><volume>72</volume><fpage>1103</fpage><lpage>1112</lpage><pub-id pub-id-type="doi">10.1002/mrm.24990</pub-id><pub-id pub-id-type="pmid">24285608</pub-id></element-citation></ref><ref id="bib54"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Joshi</surname><given-names>S</given-names></name><name><surname>Li</surname><given-names>Y</given-names></name><name><surname>Kalwani</surname><given-names>RM</given-names></name><name><surname>Gold</surname><given-names>JI</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Relationships between pupil diameter and neuronal activity in the locus coeruleus, colliculi, and cingulate cortex</article-title><source>Neuron</source><volume>89</volume><fpage>221</fpage><lpage>234</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2015.11.028</pub-id><pub-id pub-id-type="pmid">26711118</pub-id></element-citation></ref><ref id="bib55"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Juczewski</surname><given-names>K</given-names></name><name><surname>Koussa</surname><given-names>JA</given-names></name><name><surname>Kesner</surname><given-names>AJ</given-names></name><name><surname>Lee</surname><given-names>JO</given-names></name><name><surname>Lovinger</surname><given-names>DM</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Stress and behavioral correlates in the head-fixed method: stress measurements, habituation dynamics, locomotion, and motor-skill learning in mice</article-title><source>Scientific Reports</source><volume>10</volume><elocation-id>12245</elocation-id><pub-id pub-id-type="doi">10.1038/s41598-020-69132-6</pub-id><pub-id pub-id-type="pmid">32699235</pub-id></element-citation></ref><ref id="bib56"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jung</surname><given-names>WB</given-names></name><name><surname>Im</surname><given-names>GH</given-names></name><name><surname>Jiang</surname><given-names>H</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Early fMRI responses to somatosensory and optogenetic stimulation reflect neural information flow</article-title><source>PNAS</source><volume>118</volume><elocation-id>e2023265118</elocation-id><pub-id pub-id-type="doi">10.1073/pnas.2023265118</pub-id><pub-id pub-id-type="pmid">33836602</pub-id></element-citation></ref><ref id="bib57"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jung</surname><given-names>WB</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Dissection of brain-wide resting-state and functional somatosensory circuits by fMRI with optogenetic silencing</article-title><source>PNAS</source><volume>119</volume><elocation-id>e2113313119</elocation-id><pub-id pub-id-type="doi">10.1073/pnas.2113313119/-/DCSupplemental</pub-id></element-citation></ref><ref id="bib58"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kawazoe</surname><given-names>K</given-names></name><name><surname>McGlynn</surname><given-names>R</given-names></name><name><surname>Felix</surname><given-names>W</given-names></name><name><surname>Sevilla</surname><given-names>R</given-names></name><name><surname>Liao</surname><given-names>S</given-names></name><name><surname>Kulkarni</surname><given-names>P</given-names></name><name><surname>Ferris</surname><given-names>CF</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Dose-dependent effects of esketamine on brain activity in awake mice: A BOLD phMRI study</article-title><source>Pharmacology Research &amp; Perspectives</source><volume>10</volume><elocation-id>e01035</elocation-id><pub-id pub-id-type="doi">10.1002/prp2.1035</pub-id><pub-id pub-id-type="pmid">36504448</pub-id></element-citation></ref><ref id="bib59"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Keene</surname><given-names>CS</given-names></name><name><surname>Bucci</surname><given-names>DJ</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Contributions of the retrosplenial and posterior parietal cortices to cue-specific and contextual fear conditioning</article-title><source>Behavioral Neuroscience</source><volume>135</volume><fpage>693</fpage><lpage>701</lpage><pub-id pub-id-type="doi">10.1037/bne0000435</pub-id></element-citation></ref><ref id="bib60"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kwok</surname><given-names>WE</given-names></name><name><surname>You</surname><given-names>Z</given-names></name></person-group><year iso-8601-date="2006">2006</year><article-title>In vivo MRI using liquid nitrogen cooled phased array coil at 3.0 T</article-title><source>Magnetic Resonance Imaging</source><volume>24</volume><fpage>819</fpage><lpage>823</lpage><pub-id pub-id-type="doi">10.1016/j.mri.2006.01.010</pub-id><pub-id pub-id-type="pmid">16824977</pub-id></element-citation></ref><ref id="bib61"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kwong</surname><given-names>KK</given-names></name><name><surname>Belliveau</surname><given-names>JW</given-names></name><name><surname>Chesler</surname><given-names>DA</given-names></name><name><surname>Goldberg</surname><given-names>IE</given-names></name><name><surname>Weisskoff</surname><given-names>RM</given-names></name><name><surname>Poncelet</surname><given-names>BP</given-names></name><name><surname>Kennedy</surname><given-names>DN</given-names></name><name><surname>Hoppel</surname><given-names>BE</given-names></name><name><surname>Cohen</surname><given-names>MS</given-names></name><name><surname>Turner</surname><given-names>R</given-names></name></person-group><year iso-8601-date="1992">1992</year><article-title>Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation</article-title><source>PNAS</source><volume>89</volume><fpage>5675</fpage><lpage>5679</lpage><pub-id pub-id-type="doi">10.1073/pnas.89.12.5675</pub-id><pub-id pub-id-type="pmid">1608978</pub-id></element-citation></ref><ref id="bib62"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Labbé</surname><given-names>A</given-names></name><name><surname>Authelet</surname><given-names>G</given-names></name><name><surname>Baudouy</surname><given-names>B</given-names></name><name><surname>van der Beek</surname><given-names>CJ</given-names></name><name><surname>Briatico</surname><given-names>J</given-names></name><name><surname>Darrasse</surname><given-names>L</given-names></name><name><surname>Poirier-Quinot</surname><given-names>M</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Recent advances and challenges in the development of radiofrequency HTS coil for MRI</article-title><source>Frontiers in Physics</source><volume>9</volume><elocation-id>705438</elocation-id><pub-id pub-id-type="doi">10.3389/fphy.2021.705438</pub-id></element-citation></ref><ref id="bib63"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lake</surname><given-names>EMR</given-names></name><name><surname>Ge</surname><given-names>X</given-names></name><name><surname>Shen</surname><given-names>X</given-names></name><name><surname>Herman</surname><given-names>P</given-names></name><name><surname>Hyder</surname><given-names>F</given-names></name><name><surname>Cardin</surname><given-names>JA</given-names></name><name><surname>Higley</surname><given-names>MJ</given-names></name><name><surname>Scheinost</surname><given-names>D</given-names></name><name><surname>Papademetris</surname><given-names>X</given-names></name><name><surname>Crair</surname><given-names>MC</given-names></name><name><surname>Constable</surname><given-names>RT</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Simultaneous cortex-wide fluorescence Ca<sup>2+</sup> imaging and whole-brain fMRI</article-title><source>Nature Methods</source><volume>17</volume><fpage>1262</fpage><lpage>1271</lpage><pub-id pub-id-type="doi">10.1038/s41592-020-00984-6</pub-id><pub-id pub-id-type="pmid">33139894</pub-id></element-citation></ref><ref id="bib64"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>HL</given-names></name><name><surname>Li</surname><given-names>Z</given-names></name><name><surname>Coulson</surname><given-names>EJ</given-names></name><name><surname>Chuang</surname><given-names>KH</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Ultrafast fMRI of the rodent brain using simultaneous multi-slice EPI</article-title><source>NeuroImage</source><volume>195</volume><fpage>48</fpage><lpage>58</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2019.03.045</pub-id><pub-id pub-id-type="pmid">30910726</pub-id></element-citation></ref><ref id="bib65"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>JH</given-names></name><name><surname>Liu</surname><given-names>Q</given-names></name><name><surname>Dadgar-Kiani</surname><given-names>E</given-names></name></person-group><year iso-8601-date="2022">2022a</year><article-title>Solving brain circuit function and dysfunction with computational modeling and optogenetic fMRI</article-title><source>Science</source><volume>378</volume><fpage>493</fpage><lpage>499</lpage><pub-id pub-id-type="doi">10.1126/science.abq3868</pub-id><pub-id pub-id-type="pmid">36327349</pub-id></element-citation></ref><ref id="bib66"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>JY</given-names></name><name><surname>You</surname><given-names>T</given-names></name><name><surname>Woo</surname><given-names>CW</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2022">2022b</year><article-title>Optogenetic fMRI for brain-wide circuit analysis of sensory processing</article-title><source>International Journal of Molecular Sciences</source><volume>23</volume><elocation-id>12268</elocation-id><pub-id pub-id-type="doi">10.3390/ijms232012268</pub-id></element-citation></ref><ref id="bib67"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname><given-names>G</given-names></name><name><surname>Does</surname><given-names>MD</given-names></name><name><surname>Avila</surname><given-names>R</given-names></name><name><surname>Kang</surname><given-names>J</given-names></name><name><surname>Harkins</surname><given-names>KD</given-names></name><name><surname>Wu</surname><given-names>Y</given-names></name><name><surname>Banks</surname><given-names>WE</given-names></name><name><surname>Park</surname><given-names>M</given-names></name><name><surname>Lu</surname><given-names>D</given-names></name><name><surname>Yan</surname><given-names>X</given-names></name><name><surname>Kim</surname><given-names>JU</given-names></name><name><surname>Won</surname><given-names>SM</given-names></name><name><surname>Evans</surname><given-names>AG</given-names></name><name><surname>Joseph</surname><given-names>JT</given-names></name><name><surname>Kalmar</surname><given-names>CL</given-names></name><name><surname>Pollins</surname><given-names>AC</given-names></name><name><surname>Karagoz</surname><given-names>H</given-names></name><name><surname>Thayer</surname><given-names>WP</given-names></name><name><surname>Huang</surname><given-names>Y</given-names></name><name><surname>Rogers</surname><given-names>JA</given-names></name></person-group><year iso-8601-date="2024">2024</year><article-title>Implantable, bioresorbable radio frequency resonant circuits for magnetic resonance imaging</article-title><source>Advanced Science</source><volume>11</volume><elocation-id>e2301232</elocation-id><pub-id pub-id-type="doi">10.1002/advs.202301232</pub-id><pub-id pub-id-type="pmid">37357139</pub-id></element-citation></ref><ref id="bib68"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lenzi</surname><given-names>D</given-names></name><name><surname>Conte</surname><given-names>A</given-names></name><name><surname>Mainero</surname><given-names>C</given-names></name><name><surname>Frasca</surname><given-names>V</given-names></name><name><surname>Fubelli</surname><given-names>F</given-names></name><name><surname>Totaro</surname><given-names>P</given-names></name><name><surname>Caramia</surname><given-names>F</given-names></name><name><surname>Inghilleri</surname><given-names>M</given-names></name><name><surname>Pozzilli</surname><given-names>C</given-names></name><name><surname>Pantano</surname><given-names>P</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>Effect of corpus callosum damage on ipsilateral motor activation in patients with multiple sclerosis: A functional and anatomical study</article-title><source>Human Brain Mapping</source><volume>28</volume><fpage>636</fpage><lpage>644</lpage><pub-id pub-id-type="doi">10.1002/hbm.20305</pub-id><pub-id pub-id-type="pmid">17080438</pub-id></element-citation></ref><ref id="bib69"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname><given-names>Y</given-names></name><name><surname>Perez</surname><given-names>PD</given-names></name><name><surname>Ma</surname><given-names>Z</given-names></name><name><surname>Ma</surname><given-names>Z</given-names></name><name><surname>Dopfel</surname><given-names>D</given-names></name><name><surname>Cramer</surname><given-names>S</given-names></name><name><surname>Tu</surname><given-names>W</given-names></name><name><surname>Zhang</surname><given-names>N</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>An open database of resting-state fMRI in awake rats</article-title><source>NeuroImage</source><volume>220</volume><elocation-id>117094</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2020.117094</pub-id><pub-id pub-id-type="pmid">32610063</pub-id></element-citation></ref><ref id="bib70"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Logothetis</surname><given-names>NK</given-names></name><name><surname>Pauls</surname><given-names>J</given-names></name><name><surname>Augath</surname><given-names>M</given-names></name><name><surname>Trinath</surname><given-names>T</given-names></name><name><surname>Oeltermann</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2001">2001</year><article-title>Neurophysiological investigation of the basis of the fMRI signal</article-title><source>Nature</source><volume>412</volume><fpage>150</fpage><lpage>157</lpage><pub-id pub-id-type="doi">10.1038/35084005</pub-id><pub-id pub-id-type="pmid">11449264</pub-id></element-citation></ref><ref id="bib71"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Logothetis</surname><given-names>NK</given-names></name><name><surname>Merkle</surname><given-names>H</given-names></name><name><surname>Augath</surname><given-names>M</given-names></name><name><surname>Trinath</surname><given-names>T</given-names></name><name><surname>Uǧurbil</surname><given-names>K</given-names></name></person-group><year iso-8601-date="2002">2002</year><article-title>Ultra high-resolution fMRI in monkeys with implanted RF coils</article-title><source>Neuron</source><volume>35</volume><fpage>227</fpage><lpage>242</lpage><pub-id pub-id-type="doi">10.1016/S0896-6273(02)00775-4</pub-id></element-citation></ref><ref id="bib72"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Low</surname><given-names>LA</given-names></name><name><surname>Bauer</surname><given-names>LC</given-names></name><name><surname>Klaunberg</surname><given-names>BA</given-names></name></person-group><year iso-8601-date="2016">2016a</year><article-title>Comparing the effects of isoflurane and alpha chloralose upon mouse physiology</article-title><source>PLOS ONE</source><volume>11</volume><elocation-id>e0154936</elocation-id><pub-id pub-id-type="doi">10.1371/journal.pone.0154936</pub-id><pub-id pub-id-type="pmid">27148970</pub-id></element-citation></ref><ref id="bib73"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Low</surname><given-names>LA</given-names></name><name><surname>Bauer</surname><given-names>LC</given-names></name><name><surname>Pitcher</surname><given-names>MH</given-names></name><name><surname>Bushnell</surname><given-names>MC</given-names></name></person-group><year iso-8601-date="2016">2016b</year><article-title>Restraint training for awake functional brain scanning of rodents can cause long-lasting changes in pain and stress responses</article-title><source>Pain</source><volume>157</volume><fpage>1761</fpage><lpage>1772</lpage><pub-id pub-id-type="doi">10.1097/j.pain.0000000000000579</pub-id><pub-id pub-id-type="pmid">27058679</pub-id></element-citation></ref><ref id="bib74"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lu</surname><given-names>H</given-names></name><name><surname>Patel</surname><given-names>S</given-names></name><name><surname>Luo</surname><given-names>F</given-names></name><name><surname>Li</surname><given-names>S-J</given-names></name><name><surname>Hillard</surname><given-names>CJ</given-names></name><name><surname>Ward</surname><given-names>BD</given-names></name><name><surname>Hyde</surname><given-names>JS</given-names></name></person-group><year iso-8601-date="2004">2004</year><article-title>Spatial correlations of laminar BOLD and CBV responses to rat whisker stimulation with neuronal activity localized by Fos expression</article-title><source>Magnetic Resonance in Medicine</source><volume>52</volume><fpage>1060</fpage><lpage>1068</lpage><pub-id pub-id-type="doi">10.1002/mrm.20265</pub-id><pub-id pub-id-type="pmid">15508149</pub-id></element-citation></ref><ref id="bib75"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lu</surname><given-names>H</given-names></name><name><surname>Zou</surname><given-names>Q</given-names></name><name><surname>Gu</surname><given-names>H</given-names></name><name><surname>Raichle</surname><given-names>ME</given-names></name><name><surname>Stein</surname><given-names>EA</given-names></name><name><surname>Yang</surname><given-names>Y</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Rat brains also have a default mode network</article-title><source>PNAS</source><volume>109</volume><fpage>3979</fpage><lpage>3984</lpage><pub-id pub-id-type="doi">10.1073/pnas.1200506109</pub-id><pub-id pub-id-type="pmid">22355129</pub-id></element-citation></ref><ref id="bib76"><element-citation publication-type="preprint"><person-group person-group-type="author"><name><surname>Lungu</surname><given-names>R</given-names></name><name><surname>Fernandes</surname><given-names>FF</given-names></name><name><surname>Outeiro</surname><given-names>TF</given-names></name><name><surname>Shemesh</surname><given-names>N</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Brain-wide sensory aberrations in a parkinson’s disease mouse model revealed by functional MRI</article-title><source>bioRxiv</source><pub-id pub-id-type="doi">10.1101/2022.04.06.487227</pub-id></element-citation></ref><ref id="bib77"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Madularu</surname><given-names>D</given-names></name><name><surname>Kumaragamage</surname><given-names>C</given-names></name><name><surname>Mathieu</surname><given-names>AP</given-names></name><name><surname>Kulkarni</surname><given-names>P</given-names></name><name><surname>Rajah</surname><given-names>MN</given-names></name><name><surname>Gratton</surname><given-names>AP</given-names></name><name><surname>Near</surname><given-names>J</given-names></name></person-group><year iso-8601-date="2017">2017a</year><article-title>A chronic in situ coil system adapted for intracerebral stimulation during MRI in rats</article-title><source>Journal of Neuroscience Methods</source><volume>284</volume><fpage>85</fpage><lpage>95</lpage><pub-id pub-id-type="doi">10.1016/j.jneumeth.2017.04.018</pub-id><pub-id pub-id-type="pmid">28460835</pub-id></element-citation></ref><ref id="bib78"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Madularu</surname><given-names>D</given-names></name><name><surname>Mathieu</surname><given-names>AP</given-names></name><name><surname>Kumaragamage</surname><given-names>C</given-names></name><name><surname>Reynolds</surname><given-names>LM</given-names></name><name><surname>Near</surname><given-names>J</given-names></name><name><surname>Flores</surname><given-names>C</given-names></name><name><surname>Rajah</surname><given-names>MN</given-names></name></person-group><year iso-8601-date="2017">2017b</year><article-title>A non-invasive restraining system for awake mouse imaging</article-title><source>Journal of Neuroscience Methods</source><volume>287</volume><fpage>53</fpage><lpage>57</lpage><pub-id pub-id-type="doi">10.1016/j.jneumeth.2017.06.008</pub-id><pub-id pub-id-type="pmid">28634149</pub-id></element-citation></ref><ref id="bib79"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Magnuson</surname><given-names>ME</given-names></name><name><surname>Thompson</surname><given-names>GJ</given-names></name><name><surname>Pan</surname><given-names>WJ</given-names></name><name><surname>Keilholz</surname><given-names>SD</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Time-dependent effects of isoflurane and dexmedetomidine on functional connectivity, spectral characteristics, and spatial distribution of spontaneous BOLD fluctuations</article-title><source>NMR in Biomedicine</source><volume>27</volume><fpage>291</fpage><lpage>303</lpage><pub-id pub-id-type="doi">10.1002/nbm.3062</pub-id><pub-id pub-id-type="pmid">24449532</pub-id></element-citation></ref><ref id="bib80"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Mandino</surname><given-names>F</given-names></name><name><surname>Vujic</surname><given-names>S</given-names></name><name><surname>Grandjean</surname><given-names>J</given-names></name><name><surname>Lake</surname><given-names>EMR</given-names></name></person-group><year iso-8601-date="2024">2024</year><article-title>Where do we stand on fMRI in awake mice?</article-title><source>Cerebral Cortex</source><volume>34</volume><elocation-id>bhad478</elocation-id><pub-id pub-id-type="doi">10.1093/cercor/bhad478</pub-id><pub-id pub-id-type="pmid">38100331</pub-id></element-citation></ref><ref id="bib81"><element-citation publication-type="confproc"><person-group person-group-type="author"><name><surname>Marcos-Ramiro</surname><given-names>A</given-names></name><name><surname>Pizarro-Perez</surname><given-names>D</given-names></name><name><surname>Marron-Romera</surname><given-names>M</given-names></name><name><surname>Pizarro-Perez</surname><given-names>D</given-names></name><name><surname>Gatica-Perez</surname><given-names>D</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Automatic Blinking Detection towards Stress Discovery</article-title><conf-name>ICMI 2014 - Proceedings of the 2014 International Conference on Multimodal Interaction</conf-name><conf-loc>Istanbul Turkey</conf-loc><fpage>307</fpage><lpage>310</lpage><pub-id pub-id-type="doi">10.1145/2663204.2663239</pub-id></element-citation></ref><ref id="bib82"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Margalit</surname><given-names>E</given-names></name><name><surname>Jamison</surname><given-names>KW</given-names></name><name><surname>Weiner</surname><given-names>KS</given-names></name><name><surname>Vizioli</surname><given-names>L</given-names></name><name><surname>Zhang</surname><given-names>R-Y</given-names></name><name><surname>Kay</surname><given-names>KN</given-names></name><name><surname>Grill-Spector</surname><given-names>K</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Ultra-high-resolution fMRI of human ventral temporal cortex reveals differential representation of categories and domains</article-title><source>The Journal of Neuroscience</source><volume>40</volume><fpage>3008</fpage><lpage>3024</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.2106-19.2020</pub-id><pub-id pub-id-type="pmid">32094202</pub-id></element-citation></ref><ref id="bib83"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Martin</surname><given-names>LE</given-names></name><name><surname>Potts</surname><given-names>GF</given-names></name><name><surname>Burton</surname><given-names>PC</given-names></name><name><surname>Montague</surname><given-names>PR</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Electrophysiological and hemodynamic responses to reward prediction violation</article-title><source>Neuroreport</source><volume>20</volume><fpage>1140</fpage><lpage>1143</lpage><pub-id pub-id-type="doi">10.1097/WNR.0b013e32832f0dca</pub-id><pub-id pub-id-type="pmid">19690501</pub-id></element-citation></ref><ref id="bib84"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Masamoto</surname><given-names>K</given-names></name><name><surname>Kim</surname><given-names>T</given-names></name><name><surname>Fukuda</surname><given-names>M</given-names></name><name><surname>Wang</surname><given-names>P</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>Relationship between neural, vascular, and bold signals in isoflurane-anesthetized rat somatosensory cortex</article-title><source>Cerebral Cortex</source><volume>17</volume><fpage>942</fpage><lpage>950</lpage><pub-id pub-id-type="doi">10.1093/cercor/bhl005</pub-id></element-citation></ref><ref id="bib85"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McRobert</surname><given-names>AP</given-names></name><name><surname>Ward</surname><given-names>P</given-names></name><name><surname>Eccles</surname><given-names>DW</given-names></name><name><surname>Williams</surname><given-names>AM</given-names></name></person-group><year iso-8601-date="2011">2011</year><article-title>The effect of manipulating context-specific information on perceptual-cognitive processes during a simulated anticipation task</article-title><source>British Journal of Psychology</source><volume>102</volume><fpage>519</fpage><lpage>534</lpage><pub-id pub-id-type="doi">10.1111/j.2044-8295.2010.02013.x</pub-id><pub-id pub-id-type="pmid">21752003</pub-id></element-citation></ref><ref id="bib86"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Meyer</surname><given-names>AF</given-names></name><name><surname>O’Keefe</surname><given-names>J</given-names></name><name><surname>Poort</surname><given-names>J</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Two distinct types of eye-head coupling in freely moving mice</article-title><source>Current Biology</source><volume>30</volume><fpage>2116</fpage><lpage>2130</lpage><pub-id pub-id-type="doi">10.1016/j.cub.2020.04.042</pub-id><pub-id pub-id-type="pmid">32413309</pub-id></element-citation></ref><ref id="bib87"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Miller</surname><given-names>AMP</given-names></name><name><surname>Mau</surname><given-names>W</given-names></name><name><surname>Smith</surname><given-names>DM</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Retrosplenial cortical representations of space and future goal locations develop with learning</article-title><source>Current Biology</source><volume>29</volume><fpage>2083</fpage><lpage>2090</lpage><pub-id pub-id-type="doi">10.1016/j.cub.2019.05.034</pub-id><pub-id pub-id-type="pmid">31178316</pub-id></element-citation></ref><ref id="bib88"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nakamura</surname><given-names>Y</given-names></name><name><surname>Nakamura</surname><given-names>Y</given-names></name><name><surname>Pelosi</surname><given-names>A</given-names></name><name><surname>Djemai</surname><given-names>B</given-names></name><name><surname>Debacker</surname><given-names>C</given-names></name><name><surname>Hervé</surname><given-names>D</given-names></name><name><surname>Girault</surname><given-names>J-A</given-names></name><name><surname>Tsurugizawa</surname><given-names>T</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>fMRI detects bilateral brain network activation following unilateral chemogenetic activation of direct striatal projection neurons</article-title><source>NeuroImage</source><volume>220</volume><elocation-id>117079</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2020.117079</pub-id><pub-id pub-id-type="pmid">32585345</pub-id></element-citation></ref><ref id="bib89"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Niendorf</surname><given-names>T</given-names></name><name><surname>Pohlmann</surname><given-names>A</given-names></name><name><surname>Reimann</surname><given-names>HM</given-names></name><name><surname>Waiczies</surname><given-names>H</given-names></name><name><surname>Peper</surname><given-names>E</given-names></name><name><surname>Huelnhagen</surname><given-names>T</given-names></name><name><surname>Seeliger</surname><given-names>E</given-names></name><name><surname>Schreiber</surname><given-names>A</given-names></name><name><surname>Kettritz</surname><given-names>R</given-names></name><name><surname>Strobel</surname><given-names>K</given-names></name><name><surname>Ku</surname><given-names>M-C</given-names></name><name><surname>Waiczies</surname><given-names>S</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Advancing cardiovascular, neurovascular, and renal magnetic resonance imaging in small rodents using cryogenic radiofrequency coil technology</article-title><source>Frontiers in Pharmacology</source><volume>6</volume><elocation-id>255</elocation-id><pub-id pub-id-type="doi">10.3389/fphar.2015.00255</pub-id><pub-id pub-id-type="pmid">26617515</pub-id></element-citation></ref><ref id="bib90"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Niranjan</surname><given-names>A</given-names></name><name><surname>Christie</surname><given-names>IN</given-names></name><name><surname>Solomon</surname><given-names>SG</given-names></name><name><surname>Wells</surname><given-names>JA</given-names></name><name><surname>Lythgoe</surname><given-names>MF</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>fMRI mapping of the visual system in the mouse brain with interleaved snapshot GE-EPI</article-title><source>NeuroImage</source><volume>139</volume><fpage>337</fpage><lpage>345</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2016.06.015</pub-id></element-citation></ref><ref id="bib91"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ogawa</surname><given-names>S</given-names></name><name><surname>Lee</surname><given-names>TM</given-names></name><name><surname>Kay</surname><given-names>AR</given-names></name><name><surname>Tank</surname><given-names>DW</given-names></name></person-group><year iso-8601-date="1990">1990a</year><article-title>Brain magnetic resonance imaging with contrast dependent on blood oxygenation</article-title><source>PNAS</source><volume>87</volume><fpage>9868</fpage><lpage>9872</lpage><pub-id pub-id-type="doi">10.1073/pnas.87.24.9868</pub-id><pub-id pub-id-type="pmid">2124706</pub-id></element-citation></ref><ref id="bib92"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ogawa</surname><given-names>S</given-names></name><name><surname>Lee</surname><given-names>T</given-names></name><name><surname>Nayak</surname><given-names>AS</given-names></name><name><surname>Glynn</surname><given-names>P</given-names></name></person-group><year iso-8601-date="1990">1990b</year><article-title>Oxygenation‐sensitive contrast in magnetic resonance image of rodent brain at high magnetic fields</article-title><source>Magnetic Resonance in Medicine</source><volume>14</volume><fpage>68</fpage><lpage>78</lpage><pub-id pub-id-type="doi">10.1002/mrm.1910140108</pub-id></element-citation></ref><ref id="bib93"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ogawa</surname><given-names>S</given-names></name><name><surname>Tank</surname><given-names>DW</given-names></name><name><surname>Menon</surname><given-names>R</given-names></name><name><surname>Ellermann</surname><given-names>JM</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name><name><surname>Merkle</surname><given-names>H</given-names></name><name><surname>Ugurbil</surname><given-names>K</given-names></name></person-group><year iso-8601-date="1992">1992</year><article-title>Intrinsic signal changes accompanying sensory stimulation: functional brain mapping with magnetic resonance imaging</article-title><source>PNAS</source><volume>89</volume><fpage>5951</fpage><lpage>5955</lpage><pub-id pub-id-type="doi">10.1073/pnas.89.13.5951</pub-id><pub-id pub-id-type="pmid">1631079</pub-id></element-citation></ref><ref id="bib94"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Oh</surname><given-names>SW</given-names></name><name><surname>Harris</surname><given-names>JA</given-names></name><name><surname>Ng</surname><given-names>L</given-names></name><name><surname>Winslow</surname><given-names>B</given-names></name><name><surname>Cain</surname><given-names>N</given-names></name><name><surname>Mihalas</surname><given-names>S</given-names></name><name><surname>Wang</surname><given-names>Q</given-names></name><name><surname>Lau</surname><given-names>C</given-names></name><name><surname>Kuan</surname><given-names>L</given-names></name><name><surname>Henry</surname><given-names>AM</given-names></name><name><surname>Mortrud</surname><given-names>MT</given-names></name><name><surname>Ouellette</surname><given-names>B</given-names></name><name><surname>Nguyen</surname><given-names>TN</given-names></name><name><surname>Sorensen</surname><given-names>SA</given-names></name><name><surname>Slaughterbeck</surname><given-names>CR</given-names></name><name><surname>Wakeman</surname><given-names>W</given-names></name><name><surname>Li</surname><given-names>Y</given-names></name><name><surname>Feng</surname><given-names>D</given-names></name><name><surname>Ho</surname><given-names>A</given-names></name><name><surname>Nicholas</surname><given-names>E</given-names></name><name><surname>Hirokawa</surname><given-names>KE</given-names></name><name><surname>Bohn</surname><given-names>P</given-names></name><name><surname>Joines</surname><given-names>KM</given-names></name><name><surname>Peng</surname><given-names>H</given-names></name><name><surname>Hawrylycz</surname><given-names>MJ</given-names></name><name><surname>Phillips</surname><given-names>JW</given-names></name><name><surname>Hohmann</surname><given-names>JG</given-names></name><name><surname>Wohnoutka</surname><given-names>P</given-names></name><name><surname>Gerfen</surname><given-names>CR</given-names></name><name><surname>Koch</surname><given-names>C</given-names></name><name><surname>Bernard</surname><given-names>A</given-names></name><name><surname>Dang</surname><given-names>C</given-names></name><name><surname>Jones</surname><given-names>AR</given-names></name><name><surname>Zeng</surname><given-names>H</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>A mesoscale connectome of the mouse brain</article-title><source>Nature</source><volume>508</volume><fpage>207</fpage><lpage>214</lpage><pub-id pub-id-type="doi">10.1038/nature13186</pub-id><pub-id pub-id-type="pmid">24695228</pub-id></element-citation></ref><ref id="bib95"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Oyarzabal</surname><given-names>EA</given-names></name><name><surname>Hsu</surname><given-names>L-M</given-names></name><name><surname>Das</surname><given-names>M</given-names></name><name><surname>Chao</surname><given-names>T-HH</given-names></name><name><surname>Zhou</surname><given-names>J</given-names></name><name><surname>Song</surname><given-names>S</given-names></name><name><surname>Zhang</surname><given-names>W</given-names></name><name><surname>Smith</surname><given-names>KG</given-names></name><name><surname>Sciolino</surname><given-names>NR</given-names></name><name><surname>Evsyukova</surname><given-names>IY</given-names></name><name><surname>Yuan</surname><given-names>H</given-names></name><name><surname>Lee</surname><given-names>S-H</given-names></name><name><surname>Cui</surname><given-names>G</given-names></name><name><surname>Jensen</surname><given-names>P</given-names></name><name><surname>Shih</surname><given-names>Y-YI</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Chemogenetic stimulation of tonic locus coeruleus activity strengthens the default mode network</article-title><source>Science Advances</source><volume>8</volume><elocation-id>eabm9898</elocation-id><pub-id pub-id-type="doi">10.1126/sciadv.abm9898</pub-id><pub-id pub-id-type="pmid">35486721</pub-id></element-citation></ref><ref id="bib96"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Paukert</surname><given-names>M</given-names></name><name><surname>Agarwal</surname><given-names>A</given-names></name><name><surname>Cha</surname><given-names>J</given-names></name><name><surname>Doze</surname><given-names>VA</given-names></name><name><surname>Kang</surname><given-names>JU</given-names></name><name><surname>Bergles</surname><given-names>DE</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Norepinephrine controls astroglial responsiveness to local circuit activity</article-title><source>Neuron</source><volume>82</volume><fpage>1263</fpage><lpage>1270</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2014.04.038</pub-id><pub-id pub-id-type="pmid">24945771</pub-id></element-citation></ref><ref id="bib97"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pauling</surname><given-names>L</given-names></name><name><surname>Coryell</surname><given-names>CD</given-names></name></person-group><year iso-8601-date="1936">1936</year><article-title>The magnetic properties and structure of hemoglobin, oxyhemoglobin and carbonmonoxyhemoglobin</article-title><source>PNAS</source><volume>22</volume><fpage>210</fpage><lpage>216</lpage><pub-id pub-id-type="doi">10.1073/pnas.22.4.210</pub-id><pub-id pub-id-type="pmid">16577697</pub-id></element-citation></ref><ref id="bib98"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Peeters</surname><given-names>LM</given-names></name><name><surname>Hinz</surname><given-names>R</given-names></name><name><surname>Detrez</surname><given-names>JR</given-names></name><name><surname>Missault</surname><given-names>S</given-names></name><name><surname>De Vos</surname><given-names>WH</given-names></name><name><surname>Verhoye</surname><given-names>M</given-names></name><name><surname>Van der Linden</surname><given-names>A</given-names></name><name><surname>Keliris</surname><given-names>GA</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>Chemogenetic silencing of neurons in the mouse anterior cingulate area modulates neuronal activity and functional connectivity</article-title><source>NeuroImage</source><volume>220</volume><elocation-id>117088</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2020.117088</pub-id><pub-id pub-id-type="pmid">32592851</pub-id></element-citation></ref><ref id="bib99"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pérez-Cervera</surname><given-names>L</given-names></name><name><surname>Caramés</surname><given-names>JM</given-names></name><name><surname>Fernández-Mollá</surname><given-names>LM</given-names></name><name><surname>Moreno</surname><given-names>A</given-names></name><name><surname>Fernández</surname><given-names>B</given-names></name><name><surname>Pérez-Montoyo</surname><given-names>E</given-names></name><name><surname>Moratal</surname><given-names>D</given-names></name><name><surname>Canals</surname><given-names>S</given-names></name><name><surname>Pacheco-Torres</surname><given-names>J</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>Mapping functional connectivity in the rodent brain using electric-stimulation fMRI</article-title><source>Methods in Molecular Biology</source><volume>1718</volume><fpage>117</fpage><lpage>134</lpage><pub-id pub-id-type="doi">10.1007/978-1-4939-7531-0_8</pub-id><pub-id pub-id-type="pmid">29341006</pub-id></element-citation></ref><ref id="bib100"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pezzulo</surname><given-names>G</given-names></name><name><surname>Hoffmann</surname><given-names>J</given-names></name><name><surname>Falcone</surname><given-names>R</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>Anticipation and anticipatory behavior</article-title><source>Cognitive Processing</source><volume>8</volume><fpage>67</fpage><lpage>70</lpage><pub-id pub-id-type="doi">10.1007/s10339-007-0173-z</pub-id></element-citation></ref><ref id="bib101"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pfeffer</surname><given-names>T</given-names></name><name><surname>Keitel</surname><given-names>C</given-names></name><name><surname>Kluger</surname><given-names>DS</given-names></name><name><surname>Keitel</surname><given-names>A</given-names></name><name><surname>Russmann</surname><given-names>A</given-names></name><name><surname>Thut</surname><given-names>G</given-names></name><name><surname>Donner</surname><given-names>TH</given-names></name><name><surname>Gross</surname><given-names>J</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Coupling of pupil- and neuronal population dynamics reveals diverse influences of arousal on cortical processing</article-title><source>eLife</source><volume>11</volume><elocation-id>e71890</elocation-id><pub-id pub-id-type="doi">10.7554/eLife.71890</pub-id><pub-id pub-id-type="pmid">35133276</pub-id></element-citation></ref><ref id="bib102"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pirttimäki</surname><given-names>T</given-names></name><name><surname>Salo</surname><given-names>RA</given-names></name><name><surname>Shatillo</surname><given-names>A</given-names></name><name><surname>Kettunen</surname><given-names>MI</given-names></name><name><surname>Paasonen</surname><given-names>J</given-names></name><name><surname>Sierra</surname><given-names>A</given-names></name><name><surname>Jokivarsi</surname><given-names>K</given-names></name><name><surname>Leinonen</surname><given-names>V</given-names></name><name><surname>Andrade</surname><given-names>P</given-names></name><name><surname>Quittek</surname><given-names>S</given-names></name><name><surname>Pitkänen</surname><given-names>A</given-names></name><name><surname>Gröhn</surname><given-names>O</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Implantable RF-coil with multiple electrodes for long-term EEG-fMRI monitoring in rodents</article-title><source>Journal of Neuroscience Methods</source><volume>274</volume><fpage>154</fpage><lpage>163</lpage><pub-id pub-id-type="doi">10.1016/j.jneumeth.2016.10.014</pub-id><pub-id pub-id-type="pmid">27777001</pub-id></element-citation></ref><ref id="bib103"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ploghaus</surname><given-names>A</given-names></name><name><surname>Becerra</surname><given-names>L</given-names></name><name><surname>Borras</surname><given-names>C</given-names></name><name><surname>Borsook</surname><given-names>D</given-names></name></person-group><year iso-8601-date="2003">2003</year><article-title>Neural circuitry underlying pain modulation: expectation, hypnosis, placebo</article-title><source>Trends in Cognitive Sciences</source><volume>7</volume><fpage>197</fpage><lpage>200</lpage><pub-id pub-id-type="doi">10.1016/s1364-6613(03)00061-5</pub-id><pub-id pub-id-type="pmid">12757820</pub-id></element-citation></ref><ref id="bib104"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pohmann</surname><given-names>R</given-names></name><name><surname>Speck</surname><given-names>O</given-names></name><name><surname>Scheffler</surname><given-names>K</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Signal-to-noise ratio and MR tissue parameters in human brain imaging at 3, 7, and 9.4 tesla using current receive coil arrays</article-title><source>Magnetic Resonance in Medicine</source><volume>75</volume><fpage>801</fpage><lpage>809</lpage><pub-id pub-id-type="doi">10.1002/mrm.25677</pub-id><pub-id pub-id-type="pmid">25820458</pub-id></element-citation></ref><ref id="bib105"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Poskanzer</surname><given-names>KE</given-names></name><name><surname>Yuste</surname><given-names>R</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Astrocytes regulate cortical state switching in vivo</article-title><source>PNAS</source><volume>113</volume><fpage>E2675</fpage><lpage>E2684</lpage><pub-id pub-id-type="doi">10.1073/pnas.1520759113</pub-id><pub-id pub-id-type="pmid">27122314</pub-id></element-citation></ref><ref id="bib106"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Radwanska</surname><given-names>A</given-names></name><name><surname>Debowska</surname><given-names>W</given-names></name><name><surname>Liguz-Lecznar</surname><given-names>M</given-names></name><name><surname>Brzezicka</surname><given-names>A</given-names></name><name><surname>Kossut</surname><given-names>M</given-names></name><name><surname>Cybulska-Klosowicz</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2010">2010</year><article-title>Involvement of retrosplenial cortex in classical conditioning</article-title><source>Behavioural Brain Research</source><volume>214</volume><fpage>231</fpage><lpage>239</lpage><pub-id pub-id-type="doi">10.1016/j.bbr.2010.05.042</pub-id><pub-id pub-id-type="pmid">20561962</pub-id></element-citation></ref><ref id="bib107"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Raichle</surname><given-names>ME</given-names></name><name><surname>MacLeod</surname><given-names>AM</given-names></name><name><surname>Snyder</surname><given-names>AZ</given-names></name><name><surname>Powers</surname><given-names>WJ</given-names></name><name><surname>Gusnard</surname><given-names>DA</given-names></name><name><surname>Shulman</surname><given-names>GL</given-names></name></person-group><year iso-8601-date="2001">2001</year><article-title>A default mode of brain function</article-title><source>PNAS</source><volume>98</volume><fpage>676</fpage><lpage>682</lpage><pub-id pub-id-type="doi">10.1073/pnas.98.2.676</pub-id><pub-id pub-id-type="pmid">11209064</pub-id></element-citation></ref><ref id="bib108"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Reddy</surname><given-names>H</given-names></name><name><surname>Lassonde</surname><given-names>M</given-names></name><name><surname>Bemasconi</surname><given-names>N</given-names></name><name><surname>Bemasconi</surname><given-names>A</given-names></name><name><surname>Matthews</surname><given-names>PM</given-names></name><name><surname>Andermann</surname><given-names>F</given-names></name><name><surname>Amold</surname><given-names>DL</given-names></name></person-group><year iso-8601-date="2000">2000</year><article-title>An fMRI study of the lateralization of motor cortex activation in acallosal patients</article-title><source>NeuroReport</source><volume>11</volume><fpage>2409</fpage><lpage>2413</lpage><pub-id pub-id-type="doi">10.1097/00001756-200008030-00014</pub-id></element-citation></ref><ref id="bib109"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rilling</surname><given-names>JK</given-names></name><name><surname>Barks</surname><given-names>SK</given-names></name><name><surname>Parr</surname><given-names>LA</given-names></name><name><surname>Preuss</surname><given-names>TM</given-names></name><name><surname>Faber</surname><given-names>TL</given-names></name><name><surname>Pagnoni</surname><given-names>G</given-names></name><name><surname>Bremner</surname><given-names>JD</given-names></name><name><surname>Votaw</surname><given-names>JR</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>A comparison of resting-state brain activity in humans and chimpanzees</article-title><source>PNAS</source><volume>104</volume><fpage>17146</fpage><lpage>17151</lpage><pub-id pub-id-type="doi">10.1073/pnas.0705132104</pub-id><pub-id pub-id-type="pmid">17940032</pub-id></element-citation></ref><ref id="bib110"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rocchi</surname><given-names>F</given-names></name><name><surname>Canella</surname><given-names>C</given-names></name><name><surname>Noei</surname><given-names>S</given-names></name><name><surname>Gutierrez-Barragan</surname><given-names>D</given-names></name><name><surname>Coletta</surname><given-names>L</given-names></name><name><surname>Galbusera</surname><given-names>A</given-names></name><name><surname>Stuefer</surname><given-names>A</given-names></name><name><surname>Vassanelli</surname><given-names>S</given-names></name><name><surname>Pasqualetti</surname><given-names>M</given-names></name><name><surname>Iurilli</surname><given-names>G</given-names></name><name><surname>Panzeri</surname><given-names>S</given-names></name><name><surname>Gozzi</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Increased fMRI connectivity upon chemogenetic inhibition of the mouse prefrontal cortex</article-title><source>Nature Communications</source><volume>13</volume><fpage>1</fpage><lpage>15</lpage><pub-id pub-id-type="doi">10.1038/s41467-022-28591-3</pub-id></element-citation></ref><ref id="bib111"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Scheller</surname><given-names>MS</given-names></name><name><surname>Tateishi</surname><given-names>A</given-names></name><name><surname>Drummond</surname><given-names>JC</given-names></name><name><surname>Zornow</surname><given-names>MH</given-names></name></person-group><year iso-8601-date="1988">1988</year><article-title>The effects of sevoflurane on cerebral blood flow, cerebral metabolic rate for oxygen, intracranial pressure, and the electroencephalogram are similar to those of isoflurane in the rabbit</article-title><source>Anesthesiology</source><volume>68</volume><fpage>548</fpage><lpage>551</lpage><pub-id pub-id-type="doi">10.1097/00000542-198804000-00012</pub-id><pub-id pub-id-type="pmid">3354892</pub-id></element-citation></ref><ref id="bib112"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schulz</surname><given-names>K</given-names></name><name><surname>Sydekum</surname><given-names>E</given-names></name><name><surname>Krueppel</surname><given-names>R</given-names></name><name><surname>Engelbrecht</surname><given-names>CJ</given-names></name><name><surname>Schlegel</surname><given-names>F</given-names></name><name><surname>Schröter</surname><given-names>A</given-names></name><name><surname>Rudin</surname><given-names>M</given-names></name><name><surname>Helmchen</surname><given-names>F</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Simultaneous BOLD fMRI and fiber-optic calcium recording in rat neocortex</article-title><source>Nature Methods</source><volume>9</volume><fpage>597</fpage><lpage>602</lpage><pub-id pub-id-type="doi">10.1038/nmeth.2013</pub-id><pub-id pub-id-type="pmid">22561989</pub-id></element-citation></ref><ref id="bib113"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Setzer</surname><given-names>B</given-names></name><name><surname>Fultz</surname><given-names>NE</given-names></name><name><surname>Gomez</surname><given-names>DEP</given-names></name><name><surname>Williams</surname><given-names>SD</given-names></name><name><surname>Bonmassar</surname><given-names>G</given-names></name><name><surname>Polimeni</surname><given-names>JR</given-names></name><name><surname>Lewis</surname><given-names>LD</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>A temporal sequence of thalamic activity unfolds at transitions in behavioral arousal state</article-title><source>Nature Communications</source><volume>13</volume><elocation-id>5442</elocation-id><pub-id pub-id-type="doi">10.1038/s41467-022-33010-8</pub-id><pub-id pub-id-type="pmid">36114170</pub-id></element-citation></ref><ref id="bib114"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sharp</surname><given-names>PS</given-names></name><name><surname>Shaw</surname><given-names>K</given-names></name><name><surname>Boorman</surname><given-names>L</given-names></name><name><surname>Harris</surname><given-names>S</given-names></name><name><surname>Kennerley</surname><given-names>AJ</given-names></name><name><surname>Azzouz</surname><given-names>M</given-names></name><name><surname>Berwick</surname><given-names>J</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Comparison of stimulus-evoked cerebral hemodynamics in the awake mouse and under a novel anesthetic regime</article-title><source>Scientific Reports</source><volume>5</volume><elocation-id>12621</elocation-id><pub-id pub-id-type="doi">10.1038/srep12621</pub-id><pub-id pub-id-type="pmid">26218081</pub-id></element-citation></ref><ref id="bib115"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shih</surname><given-names>AY</given-names></name><name><surname>Drew</surname><given-names>PJ</given-names></name><name><surname>Kleinfeld</surname><given-names>D</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>Imaging vasodynamics in the awake mouse brain with two-photon microscopy</article-title><source>Neuromethods</source><volume>88</volume><fpage>55</fpage><lpage>73</lpage><pub-id pub-id-type="doi">10.1007/978-1-4939-0724-3_4</pub-id></element-citation></ref><ref id="bib116"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shim</surname><given-names>H-J</given-names></name><name><surname>Jung</surname><given-names>WB</given-names></name><name><surname>Schlegel</surname><given-names>F</given-names></name><name><surname>Lee</surname><given-names>J</given-names></name><name><surname>Kim</surname><given-names>S</given-names></name><name><surname>Lee</surname><given-names>J</given-names></name><name><surname>Kim</surname><given-names>S-G</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>Mouse fMRI under ketamine and xylazine anesthesia: Robust contralateral somatosensory cortex activation in response to forepaw stimulation</article-title><source>NeuroImage</source><volume>177</volume><fpage>30</fpage><lpage>44</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2018.04.062</pub-id><pub-id pub-id-type="pmid">29730495</pub-id></element-citation></ref><ref id="bib117"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shim</surname><given-names>HJ</given-names></name><name><surname>Lee</surname><given-names>J</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2020">2020</year><article-title>BOLD fMRI and hemodynamic responses to somatosensory stimulation in anesthetized mice: spontaneous breathing vs. mechanical ventilation</article-title><source>NMR in Biomedicine</source><volume>33</volume><elocation-id>e4311</elocation-id><pub-id pub-id-type="doi">10.1002/nbm.4311</pub-id><pub-id pub-id-type="pmid">32297409</pub-id></element-citation></ref><ref id="bib118"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Siegel</surname><given-names>JJ</given-names></name><name><surname>Taylor</surname><given-names>W</given-names></name><name><surname>Gray</surname><given-names>R</given-names></name><name><surname>Kalmbach</surname><given-names>B</given-names></name><name><surname>Zemelman</surname><given-names>BV</given-names></name><name><surname>Desai</surname><given-names>NS</given-names></name><name><surname>Johnston</surname><given-names>D</given-names></name><name><surname>Chitwood</surname><given-names>RA</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Trace eyeblink conditioning in mice is dependent upon the dorsal medial prefrontal cortex, cerebellum, and amygdala: behavioral characterization and functional circuitry</article-title><source>eNeuro</source><volume>2</volume><fpage>51</fpage><lpage>65</lpage><pub-id pub-id-type="doi">10.1523/ENEURO.0051-14.2015</pub-id><pub-id pub-id-type="pmid">26464998</pub-id></element-citation></ref><ref id="bib119"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sirotin</surname><given-names>YB</given-names></name><name><surname>Das</surname><given-names>A</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Anticipatory haemodynamic signals in sensory cortex not predicted by local neuronal activity</article-title><source>Nature</source><volume>457</volume><fpage>475</fpage><lpage>479</lpage><pub-id pub-id-type="doi">10.1038/nature07664</pub-id><pub-id pub-id-type="pmid">19158795</pub-id></element-citation></ref><ref id="bib120"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Smith</surname><given-names>DM</given-names></name><name><surname>Miller</surname><given-names>AMP</given-names></name><name><surname>Vedder</surname><given-names>LC</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>The retrosplenial cortical role in encoding behaviorally significant cues</article-title><source>Behavioral Neuroscience</source><volume>132</volume><fpage>356</fpage><lpage>365</lpage><pub-id pub-id-type="doi">10.1037/bne0000257</pub-id></element-citation></ref><ref id="bib121"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Srinivasan</surname><given-names>R</given-names></name><name><surname>Huang</surname><given-names>BS</given-names></name><name><surname>Venugopal</surname><given-names>S</given-names></name><name><surname>Johnston</surname><given-names>AD</given-names></name><name><surname>Chai</surname><given-names>H</given-names></name><name><surname>Zeng</surname><given-names>H</given-names></name><name><surname>Golshani</surname><given-names>P</given-names></name><name><surname>Khakh</surname><given-names>BS</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Ca(2+) signaling in astrocytes from IP3R2(-/-) mice in brain slices and during startle responses in vivo</article-title><source>Nature Neuroscience</source><volume>18</volume><fpage>708</fpage><lpage>717</lpage><pub-id pub-id-type="doi">10.1038/nn.4001</pub-id><pub-id pub-id-type="pmid">25894291</pub-id></element-citation></ref><ref id="bib122"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Steiner</surname><given-names>AR</given-names></name><name><surname>Rousseau-Blass</surname><given-names>F</given-names></name><name><surname>Schroeter</surname><given-names>A</given-names></name><name><surname>Hartnack</surname><given-names>S</given-names></name><name><surname>Bettschart-Wolfensberger</surname><given-names>R</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Systematic review: anesthetic protocols and management as confounders in rodent blood oxygen level dependent functional magnetic resonance imaging (BOLD fMRI)-Part B: effects of anesthetic agents, doses and timing</article-title><source>Animals</source><volume>11</volume><elocation-id>199</elocation-id><pub-id pub-id-type="doi">10.3390/ani11010199</pub-id><pub-id pub-id-type="pmid">33467584</pub-id></element-citation></ref><ref id="bib123"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Summers</surname><given-names>RM</given-names></name><name><surname>Hedlund</surname><given-names>LW</given-names></name><name><surname>Cofer</surname><given-names>GP</given-names></name><name><surname>Gottsman</surname><given-names>MB</given-names></name><name><surname>Manibo</surname><given-names>JF</given-names></name><name><surname>Johnson</surname><given-names>GA</given-names></name></person-group><year iso-8601-date="1995">1995</year><article-title>MR microscopy of the rat carotid artery after balloon injury by using an implanted imaging coil</article-title><source>Magnetic Resonance in Medicine</source><volume>33</volume><fpage>785</fpage><lpage>789</lpage><pub-id pub-id-type="doi">10.1002/mrm.1910330607</pub-id><pub-id pub-id-type="pmid">7651114</pub-id></element-citation></ref><ref id="bib124"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Takata</surname><given-names>N</given-names></name><name><surname>Yoshida</surname><given-names>K</given-names></name><name><surname>Komaki</surname><given-names>Y</given-names></name><name><surname>Xu</surname><given-names>M</given-names></name><name><surname>Sakai</surname><given-names>Y</given-names></name><name><surname>Hikishima</surname><given-names>K</given-names></name><name><surname>Mimura</surname><given-names>M</given-names></name><name><surname>Okano</surname><given-names>H</given-names></name><name><surname>Tanaka</surname><given-names>KF</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Optogenetic activation of CA1 pyramidal neurons at the dorsal and ventral hippocampus evokes distinct brain-wide responses revealed by mouse fMRI</article-title><source>PLOS ONE</source><volume>10</volume><elocation-id>e0121417</elocation-id><pub-id pub-id-type="doi">10.1371/journal.pone.0121417</pub-id><pub-id pub-id-type="pmid">25793741</pub-id></element-citation></ref><ref id="bib125"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Takata</surname><given-names>N</given-names></name><name><surname>Sugiura</surname><given-names>Y</given-names></name><name><surname>Yoshida</surname><given-names>K</given-names></name><name><surname>Koizumi</surname><given-names>M</given-names></name><name><surname>Hiroshi</surname><given-names>N</given-names></name><name><surname>Honda</surname><given-names>K</given-names></name><name><surname>Yano</surname><given-names>R</given-names></name><name><surname>Komaki</surname><given-names>Y</given-names></name><name><surname>Matsui</surname><given-names>K</given-names></name><name><surname>Suematsu</surname><given-names>M</given-names></name><name><surname>Mimura</surname><given-names>M</given-names></name><name><surname>Okano</surname><given-names>H</given-names></name><name><surname>Tanaka</surname><given-names>KF</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>Optogenetic astrocyte activation evokes BOLD fMRI response with oxygen consumption without neuronal activity modulation</article-title><source>Glia</source><volume>66</volume><fpage>2013</fpage><lpage>2023</lpage><pub-id pub-id-type="doi">10.1002/glia.23454</pub-id><pub-id pub-id-type="pmid">29845643</pub-id></element-citation></ref><ref id="bib126"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Taube</surname><given-names>JS</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>The head direction signal: origins and sensory-motor integration</article-title><source>Annual Review of Neuroscience</source><volume>30</volume><fpage>181</fpage><lpage>207</lpage><pub-id pub-id-type="doi">10.1146/annurev.neuro.29.051605.112854</pub-id><pub-id pub-id-type="pmid">17341158</pub-id></element-citation></ref><ref id="bib127"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Todd</surname><given-names>TP</given-names></name><name><surname>Fournier</surname><given-names>DI</given-names></name><name><surname>Bucci</surname><given-names>DJ</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Retrosplenial cortex and its role in cue-specific learning and memory</article-title><source>Neuroscience and Biobehavioral Reviews</source><volume>107</volume><fpage>713</fpage><lpage>728</lpage><pub-id pub-id-type="doi">10.1016/j.neubiorev.2019.04.016</pub-id><pub-id pub-id-type="pmid">31055014</pub-id></element-citation></ref><ref id="bib128"><element-citation publication-type="confproc"><person-group person-group-type="author"><name><surname>Tong</surname><given-names>C</given-names></name><name><surname>Zou</surname><given-names>Y</given-names></name><name><surname>Xia</surname><given-names>Y</given-names></name><name><surname>Li</surname><given-names>W</given-names></name><name><surname>Liang</surname><given-names>Z</given-names></name></person-group><year iso-8601-date="2024">2024</year><article-title>Astrocytic calcium signal bidirectionally regulated BOLD-fMRI signals in awake mice</article-title><conf-name>Proceedings of the International Society for Magnetic Resonance in Medicine</conf-name><fpage>32</fpage></element-citation></ref><ref id="bib129"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tsurugizawa</surname><given-names>T</given-names></name><name><surname>Yoshimaru</surname><given-names>D</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Impact of anesthesia on static and dynamic functional connectivity in mice</article-title><source>NeuroImage</source><volume>241</volume><elocation-id>118413</elocation-id><pub-id pub-id-type="doi">10.1016/j.neuroimage.2021.118413</pub-id><pub-id pub-id-type="pmid">34293463</pub-id></element-citation></ref><ref id="bib130"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Valerio</surname><given-names>S</given-names></name><name><surname>Taube</surname><given-names>JS</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>Path integration: how the head direction signal maintains and corrects spatial orientation</article-title><source>Nature Neuroscience</source><volume>15</volume><fpage>1445</fpage><lpage>1453</lpage><pub-id pub-id-type="doi">10.1038/nn.3215</pub-id><pub-id pub-id-type="pmid">22983210</pub-id></element-citation></ref><ref id="bib131"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Van der Knaap</surname><given-names>N</given-names></name><name><surname>Wiedermann</surname><given-names>D</given-names></name><name><surname>Schubert</surname><given-names>D</given-names></name><name><surname>Hoehn</surname><given-names>M</given-names></name><name><surname>Homberg</surname><given-names>JR</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Perinatal SSRI exposure affects brain functional activity associated with whisker stimulation in adolescent and adult rats</article-title><source>Scientific Reports</source><volume>11</volume><elocation-id>1680</elocation-id><pub-id pub-id-type="doi">10.1038/s41598-021-81327-z</pub-id><pub-id pub-id-type="pmid">33462357</pub-id></element-citation></ref><ref id="bib132"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Vincent</surname><given-names>JL</given-names></name><name><surname>Patel</surname><given-names>GH</given-names></name><name><surname>Fox</surname><given-names>MD</given-names></name><name><surname>Snyder</surname><given-names>AZ</given-names></name><name><surname>Baker</surname><given-names>JT</given-names></name><name><surname>Van Essen</surname><given-names>DC</given-names></name><name><surname>Zempel</surname><given-names>JM</given-names></name><name><surname>Snyder</surname><given-names>LH</given-names></name><name><surname>Corbetta</surname><given-names>M</given-names></name><name><surname>Raichle</surname><given-names>ME</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>Intrinsic functional architecture in the anaesthetized monkey brain</article-title><source>Nature</source><volume>447</volume><fpage>83</fpage><lpage>86</lpage><pub-id pub-id-type="doi">10.1038/nature05758</pub-id><pub-id pub-id-type="pmid">17476267</pub-id></element-citation></ref><ref id="bib133"><element-citation publication-type="confproc"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>R</given-names></name><name><surname>Dong</surname><given-names>CM</given-names></name><name><surname>Wu</surname><given-names>EX</given-names></name><name><surname>Roberts</surname><given-names>RC</given-names></name><name><surname>Jiang</surname><given-names>LJ</given-names></name></person-group><year iso-8601-date="2018">2018a</year><article-title>Circuitry design and magnetic susceptibility evaluation of 7T fMRI implantable RF coil</article-title><conf-name>2018 International Applied Computational Electromagnetics Society Symposium (ACES</conf-name><conf-loc>Denver, CO</conf-loc><pub-id pub-id-type="doi">10.23919/ROPACES.2018.8364248</pub-id></element-citation></ref><ref id="bib134"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>M</given-names></name><name><surname>He</surname><given-names>Y</given-names></name><name><surname>Sejnowski</surname><given-names>TJ</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2018">2018b</year><article-title>Brain-state dependent astrocytic Ca<sup>2+</sup> signals are coupled to both positive and negative BOLD-fMRI signals</article-title><source>PNAS</source><volume>115</volume><fpage>E1647</fpage><lpage>E1656</lpage><pub-id pub-id-type="doi">10.1073/pnas.1711692115</pub-id><pub-id pub-id-type="pmid">29382752</pub-id></element-citation></ref><ref id="bib135"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wright</surname><given-names>AC</given-names></name><name><surname>Song</surname><given-names>HK</given-names></name><name><surname>Wehrli</surname><given-names>FW</given-names></name></person-group><year iso-8601-date="2000">2000</year><article-title>In vivo MR micro imaging with conventional radiofrequency coils cooled to 77K</article-title><source>Magnetic Resonance in Medicine</source><volume>43</volume><fpage>163</fpage><lpage>169</lpage><pub-id pub-id-type="doi">10.1002/(SICI)1522-2594(200002)43:2&lt;163::AID-MRM1&gt;3.0.CO;2-K</pub-id></element-citation></ref><ref id="bib136"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wyass</surname><given-names>JM</given-names></name><name><surname>Van Groen</surname><given-names>T</given-names></name></person-group><year iso-8601-date="1992">1992</year><article-title>Connections between the retrosplenial cortex and the hippocampal formation in the rat: A review</article-title><source>Hippocampus</source><volume>2</volume><fpage>1</fpage><lpage>11</lpage><pub-id pub-id-type="doi">10.1002/hipo.450020102</pub-id></element-citation></ref><ref id="bib137"><element-citation publication-type="preprint"><person-group person-group-type="author"><name><surname>Xu</surname><given-names>W</given-names></name><name><surname>Pei</surname><given-names>M</given-names></name><name><surname>Zhang</surname><given-names>K</given-names></name><name><surname>Tong</surname><given-names>C</given-names></name><name><surname>Bo</surname><given-names>B</given-names></name><name><surname>Feng</surname><given-names>J</given-names></name><name><surname>Zhang</surname><given-names>X-Y</given-names></name><name><surname>Liang</surname><given-names>Z</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>A systematically optimized awake mouse fMRI paradigm</article-title><source>bioRxiv</source><pub-id pub-id-type="doi">10.1101/2022.11.16.516376</pub-id></element-citation></ref><ref id="bib138"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yoshida</surname><given-names>K</given-names></name><name><surname>Mimura</surname><given-names>Y</given-names></name><name><surname>Ishihara</surname><given-names>R</given-names></name><name><surname>Nishida</surname><given-names>H</given-names></name><name><surname>Komaki</surname><given-names>Y</given-names></name><name><surname>Minakuchi</surname><given-names>T</given-names></name><name><surname>Tsurugizawa</surname><given-names>T</given-names></name><name><surname>Mimura</surname><given-names>M</given-names></name><name><surname>Okano</surname><given-names>H</given-names></name><name><surname>Tanaka</surname><given-names>KF</given-names></name><name><surname>Takata</surname><given-names>N</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Physiological effects of a habituation procedure for functional MRI in awake mice using a cryogenic radiofrequency probe</article-title><source>Journal of Neuroscience Methods</source><volume>274</volume><fpage>38</fpage><lpage>48</lpage><pub-id pub-id-type="doi">10.1016/j.jneumeth.2016.09.013</pub-id><pub-id pub-id-type="pmid">27702586</pub-id></element-citation></ref><ref id="bib139"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>You</surname><given-names>T</given-names></name><name><surname>Im</surname><given-names>GH</given-names></name><name><surname>Kim</surname><given-names>SG</given-names></name></person-group><year iso-8601-date="2021">2021</year><article-title>Characterization of brain-wide somatosensory BOLD fMRI in mice under dexmedetomidine/isoflurane and ketamine/xylazine</article-title><source>Scientific Reports</source><volume>11</volume><elocation-id>13110</elocation-id><pub-id pub-id-type="doi">10.1038/s41598-021-92582-5</pub-id><pub-id pub-id-type="pmid">34162952</pub-id></element-citation></ref><ref id="bib140"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yu</surname><given-names>X</given-names></name><name><surname>He</surname><given-names>Y</given-names></name><name><surname>Wang</surname><given-names>M</given-names></name><name><surname>Merkle</surname><given-names>H</given-names></name><name><surname>Dodd</surname><given-names>SJ</given-names></name><name><surname>Silva</surname><given-names>AC</given-names></name><name><surname>Koretsky</surname><given-names>AP</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Sensory and optogenetically driven single-vessel fMRI</article-title><source>Nature Methods</source><volume>13</volume><fpage>337</fpage><lpage>340</lpage><pub-id pub-id-type="doi">10.1038/nmeth.3765</pub-id><pub-id pub-id-type="pmid">26855362</pub-id></element-citation></ref><ref id="bib141"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yu</surname><given-names>Y</given-names></name><name><surname>Huber</surname><given-names>L</given-names></name><name><surname>Yang</surname><given-names>J</given-names></name><name><surname>Jangraw</surname><given-names>DC</given-names></name><name><surname>Handwerker</surname><given-names>DA</given-names></name><name><surname>Molfese</surname><given-names>PJ</given-names></name><name><surname>Chen</surname><given-names>G</given-names></name><name><surname>Ejima</surname><given-names>Y</given-names></name><name><surname>Wu</surname><given-names>J</given-names></name><name><surname>Bandettini</surname><given-names>PA</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Layer-specific activation of sensory input and predictive feedback in the human primary somatosensory cortex</article-title><source>Science Advances</source><volume>5</volume><elocation-id>eaav9053</elocation-id><pub-id pub-id-type="doi">10.1126/sciadv.aav9053</pub-id><pub-id pub-id-type="pmid">31106273</pub-id></element-citation></ref><ref id="bib142"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zeng</surname><given-names>H</given-names></name><name><surname>Jiang</surname><given-names>Y</given-names></name><name><surname>Beer-Hammer</surname><given-names>S</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>Awake mouse fMRI and pupillary recordings in the ultra-high magnetic field</article-title><source>Frontiers in Neuroscience</source><volume>16</volume><elocation-id>886709</elocation-id><pub-id pub-id-type="doi">10.3389/fnins.2022.886709</pub-id></element-citation></ref><ref id="bib143"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zerbi</surname><given-names>V</given-names></name><name><surname>Floriou-Servou</surname><given-names>A</given-names></name><name><surname>Markicevic</surname><given-names>M</given-names></name><name><surname>Vermeiren</surname><given-names>Y</given-names></name><name><surname>Sturman</surname><given-names>O</given-names></name><name><surname>Privitera</surname><given-names>M</given-names></name><name><surname>von Ziegler</surname><given-names>L</given-names></name><name><surname>Ferrari</surname><given-names>KD</given-names></name><name><surname>Weber</surname><given-names>B</given-names></name><name><surname>De Deyn</surname><given-names>PP</given-names></name><name><surname>Wenderoth</surname><given-names>N</given-names></name><name><surname>Bohacek</surname><given-names>J</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Rapid reconfiguration of the functional connectome after chemogenetic locus coeruleus activation</article-title><source>Neuron</source><volume>103</volume><fpage>702</fpage><lpage>718</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2019.05.034</pub-id></element-citation></ref><ref id="bib144"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhao</surname><given-names>F</given-names></name><name><surname>Zhao</surname><given-names>T</given-names></name><name><surname>Zhou</surname><given-names>L</given-names></name><name><surname>Wu</surname><given-names>Q</given-names></name><name><surname>Hu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2008">2008</year><article-title>BOLD study of stimulation-induced neural activity and resting-state connectivity in medetomidine-sedated rat</article-title><source>NeuroImage</source><volume>39</volume><fpage>248</fpage><lpage>260</lpage><pub-id pub-id-type="doi">10.1016/j.neuroimage.2007.07.063</pub-id><pub-id pub-id-type="pmid">17904868</pub-id></element-citation></ref><ref id="bib145"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhao</surname><given-names>C</given-names></name><name><surname>Guo</surname><given-names>J</given-names></name><name><surname>Li</surname><given-names>D</given-names></name><name><surname>Tao</surname><given-names>Y</given-names></name><name><surname>Ding</surname><given-names>Y</given-names></name><name><surname>Liu</surname><given-names>H</given-names></name><name><surname>Song</surname><given-names>Y</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Anticipatory alpha oscillation predicts attentional selection and hemodynamic response</article-title><source>Human Brain Mapping</source><volume>40</volume><fpage>3606</fpage><lpage>3619</lpage><pub-id pub-id-type="doi">10.1002/hbm.24619</pub-id><pub-id pub-id-type="pmid">31062891</pub-id></element-citation></ref><ref id="bib146"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhao</surname><given-names>C</given-names></name><name><surname>Li</surname><given-names>D</given-names></name><name><surname>Guo</surname><given-names>J</given-names></name><name><surname>Li</surname><given-names>B</given-names></name><name><surname>Kong</surname><given-names>Y</given-names></name><name><surname>Hu</surname><given-names>Y</given-names></name><name><surname>Du</surname><given-names>B</given-names></name><name><surname>Ding</surname><given-names>Y</given-names></name><name><surname>Li</surname><given-names>X</given-names></name><name><surname>Liu</surname><given-names>H</given-names></name><name><surname>Song</surname><given-names>Y</given-names></name></person-group><year iso-8601-date="2022">2022</year><article-title>The neurovascular couplings between electrophysiological and hemodynamic activities in anticipatory selective attention</article-title><source>Cerebral Cortex</source><volume>32</volume><fpage>4953</fpage><lpage>4968</lpage><pub-id pub-id-type="doi">10.1093/cercor/bhab525</pub-id><pub-id pub-id-type="pmid">35076708</pub-id></element-citation></ref><ref id="bib147"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Zhou</surname><given-names>XA</given-names></name><name><surname>Jiang</surname><given-names>Y</given-names></name><name><surname>Man</surname><given-names>W</given-names></name><name><surname>Yu</surname><given-names>X</given-names></name></person-group><year iso-8601-date="2023">2023</year><article-title>Multimodal methods to help interpret resting-state fmri</article-title><source>Advances in Resting-State Functional MRI: Methods, Interpretation, and Applications</source><volume>1</volume><fpage>207</fpage><lpage>235</lpage><pub-id pub-id-type="doi">10.1016/B978-0-323-91688-2.00007-2</pub-id></element-citation></ref></ref-list></back><sub-article article-type="editor-report" id="sa0"><front-stub><article-id pub-id-type="doi">10.7554/eLife.95528.3.sa0</article-id><title-group><article-title>eLife Assessment</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lerch</surname><given-names>Jason P</given-names></name><role specific-use="editor">Reviewing Editor</role><aff><institution>University of Oxford</institution><country>United Kingdom</country></aff></contrib></contrib-group><kwd-group kwd-group-type="evidence-strength"><kwd>Convincing</kwd></kwd-group><kwd-group kwd-group-type="claim-importance"><kwd>Valuable</kwd></kwd-group></front-stub><body><p>This is a <bold>valuable</bold> study describing an implementation of awake mouse fMRI with implanted head coils at high fields. The evidence presented is <bold>convincing</bold>, combining technical advances with interesting neuroscience applications showing that mice anticipate stimuli given at regular (but at irregular) intervals.</p></body></sub-article><sub-article article-type="referee-report" id="sa1"><front-stub><article-id pub-id-type="doi">10.7554/eLife.95528.3.sa1</article-id><title-group><article-title>Reviewer #1 (Public review):</article-title></title-group><contrib-group><contrib contrib-type="author"><anonymous/><role specific-use="referee">Reviewer</role></contrib></contrib-group></front-stub><body><p>Summary:</p><p>The authors bring together implanted radiofrequency coils, high-field MRI imaging, awake animal imaging, and sensory stimulation methods in a technological demonstration. The results are very detailed descriptions of the sensory systems under investigation.</p><p>Strengths:</p><p>The maps are qualitatively excellent for rodent whole-brain imaging.</p><p>The design of the holder and the coil is pretty clever.</p><p>Weaknesses:</p><p>Some unexpected regions appear on the whole brain maps, and the discussion of these regions is succinct.</p><p>The authors do not make the work and effort to train the animals and average the data from several hundred trials apparent enough. This is important for any reader who would like to consider implementing this technology.</p><p>The data is not available. This does not let the readers make their own assessment of the results.</p><p>Comments on revisions:</p><p>All good, I can but only congratulate the authors on a study well done.</p></body></sub-article><sub-article article-type="referee-report" id="sa2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.95528.3.sa2</article-id><title-group><article-title>Reviewer #2 (Public review):</article-title></title-group><contrib-group><contrib contrib-type="author"><anonymous/><role specific-use="referee">Reviewer</role></contrib></contrib-group></front-stub><body><p>This work explores the advancement of awake mouse BOLD-fMRI at 14 Tesla. The study introduces custom-implanted RF coils aimed at improving signal-to-noise ratio (SNR) and assesses their performance in detecting responses to stimuli in awake mice. The coils show significant SNR improvements and are a noteworthy innovation. Detailed descriptions of the coil design, including parts lists and diagrams, enhance the reproducibility of the methods. A thorough 5-week acclimation protocol was used to minimize stress and motion during imaging. Stress was primarily evaluated using eye tracking which, in an fMRI setting, is novel and could help move the field forward with further validation (within the context of fMRI experiments). Overall, the authors successfully demonstrate high-resolution awake mouse fMRI with enhanced SNR; thus achieving their primary aim.</p><p>This work is likely to significantly impact the field by demonstrating the feasibility of high-quality awake mouse fMRI, potentially leading to more accurate and artifact-free studies of brain function. The detailed methods shared will facilitate replication and adoption by other researchers, promoting standardized practices. The methods and data provided serve as valuable resources for the neuroscience community.</p></body></sub-article><sub-article article-type="author-comment" id="sa3"><front-stub><article-id pub-id-type="doi">10.7554/eLife.95528.3.sa3</article-id><title-group><article-title>Author response</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hike</surname><given-names>David</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Xiaochen</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Xie</surname><given-names>Zeping</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Bei</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Choi</surname><given-names>Sangcheon</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Xiaoqing Alice</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Andy</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Boston Univeristy</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Murstein</surname><given-names>Alyssa</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Boston Univeristy</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Jiang</surname><given-names>Yuanyuan</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Devor</surname><given-names>Anna</given-names></name><role specific-use="author">Author</role><aff><institution>Boston University</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Xin</given-names></name><role specific-use="author">Author</role><aff><institution>Athinoula A. Martinos Center for Biomedical Imaging; Boston Univeristy</institution><addr-line><named-content content-type="city">Boston</named-content></addr-line><country>United States</country></aff></contrib></contrib-group></front-stub><body><p>The following is the authors’ response to the original reviews.</p><disp-quote content-type="editor-comment"><p><bold>Public Reviews:</bold></p><p><bold>Reviewer #1 (Public Review):</bold></p><p>Summary:</p><p>The authors bring together implanted radiofrequency coils, high-field MRI imaging, awake animal imaging, and sensory stimulation methods in a technological demonstration. The results are very detailed descriptions of the sensory systems under investigation.</p><p>Strengths:</p><p>- The maps are qualitatively excellent for rodent whole-brain imaging. - The design of the holder and the coil is pretty clever.</p><p>Weaknesses:</p><p>- Some unexpected regions appear on the whole brain maps, and the discussion of these regions is succinct.</p><p>- The authors do not make the work and effort to train the animals and average the data from several hundred trials apparent enough. This is important for any reader who would like to consider implementing this technology.</p><p>- The data is not available. This does not let the readers make their own assessment of the results.</p></disp-quote><p>Thank you for the comments on this manuscript. We have provided more detailed discussion of the unexpected regions(page 18 – line 491-494) and training procedures(page7-9 – line 172-236). We also uploaded the datasets to OpenNeuro</p><p>Whisker (https://doi.org/10.18112/openneuro.ds005496.v1.0.1), Visual (https://doi.org/10.18112/openneuro.ds005497.v1.0.0) and Zenodo:</p><p>SNR Line Profile Data &amp; Data Processing Scripts: (https://zenodo.org/doi/10.5281/zenodo.13821455).</p><disp-quote content-type="editor-comment"><p><bold>Reviewer #2 (Public Review):</bold></p><p>Summary:</p><p>The manuscript by Hike et al. entitled 'High-resolution awake mouse fMRI at 14 Tesla' describes the implementation of awake mouse BOLD-fMRI at high field. This work is timely as the field of mouse fMRI is working toward collecting high-quality data from awake animals. Imaging awake subjects offers opportunities to study brain function that are otherwise not possible under the more common anesthetized conditions. Not to mention the confounding effects that anesthesia has on neurovascular coupling. What has made progress in this area slow (relative to other imaging approaches like optical imaging) is the environment within the MRI scanner (high acoustic noise) - as well as the intolerance of head and body motion. This work adds to a relatively small, but quickly growing literature on awake mouse fMRI. The findings in the study include testing of an implanted head-coil (for MRI data reception). Two designs are described and the SNR of these units at 9.4T and 14T are reported. Further, responses to visual as well as whisker stimulation recorded in acclimated awake mice are shown. The most interesting finding, and most novel, is the observation that mice seem to learn to anticipate the presentation of the stimulus - as demonstrated by activations evident ~6 seconds prior to the presentation of the stimulus when stimuli are delivered at regular intervals (but not when stimuli are presented at random intervals). These kinds of studies are very challenging to do. The surgical preparation and length of time invested into training animals are grueling. I also see this work as a step in the right direction and evidence of the foundations for lots of interesting future work. However, I also found a few shortcomings listed below.</p><p>Weaknesses:</p><p>(1) The surface coil, although offering a great SNR boost at the surface, ultimately comes at a cost of lower SNR in deeper more removed brain regions in comparison to commercially available Bruker coils (at room temperature). This should be quantified. A rough comparison in SNR is drawn between the implanted coils and the Bruker Cryoprobe - this should be a quantitative comparison (if possible) - including any differences in SNR in deeper brain structures. There are drawbacks to the Cryoprobe, which can be discussed, but a more thorough comparison between the implanted coils, and other existing options should be provided the Cryoprobe has been used previously in awake mouse experiments (Sensory evoked fMRI paradigms in awake mice - Chen, Physiological effects of a habituation procedure for functional MRI in awake mice using a cryogenic radiofrequency probe – Yoshida, PREVIOUS REFERENCE). Further, the details of how to build the implanted coils should be provided (shared) - this should include a parts list as well as detailed instructions on how to build the units. Also, how expensive are they? And can they be reused?</p></disp-quote><p>Thank you for the comment. We did not use a Bruker Cryoprobe for this work but rather a Bruker 4array surface coil. We are unable to compare to a cryoprobe since we do not have access to one for our system. A comparison to previously published data using different scanners could be possible but would require the sequence contain identical parameters to avoid introducing an uncontrollable variable, we are planning to recruit different laboratories to test the implanted RF coils with their existing cryoprobes in the future study.</p><p>We have included an updated figure comparing SNR at different depths across the Bruker 4-array coil and the implanted RF coils. As shown in <xref ref-type="fig" rid="fig1s2">Figure 1 - Figure Supplement 2</xref>, there is significant SNR enhancement up to 4 mm cortical depth for both single loop and ‘figure 8’ implanted RF coils in comparison to the Bruker 4-array coil.</p><fig id="sa3fig1" position="float"><label>Author response image 1.</label><caption><title>Comparison between implanted and commercial coils.</title><p>(<bold>A</bold>) shows representative coils in the single loop (left) and ‘figure 8’ styles (right). Supplementary Table 1 provides a parts list and cost for making these coils and Supplementary Figure 1 provides a circuit diagram to assemble. (<bold>B</bold>) presents the SNR line profile values as a function of distance from Pia Matter for each coil tested at 9.4T: commercial phased array surface coil (4 Array), implanted single loop coil, and implanted ‘figure 8’ coil. SNR values were calculated by dividing the signal by the standard deviation of the noise. (<bold>C-E</bold>) show a representative FLASH image with line profile of SNR measurements from each of the coils used to create the graph seen in <bold>B</bold>. Clear visual improvement in SNR can be seen in figures <bold>C-E</bold>. C – Commercial phased array. D – Single loop at 9.4T. E – Figure 8 at 9.4T. (N4 array = 6, Nsingle loop = 5, Nfigure 8 = 5)</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-sa3-fig1-v1.tif"/></fig><p>Additionally, we have added a supplementary figure (<xref ref-type="fig" rid="fig1s1">Figure 1 - Figure Supplement 1</xref>) of a circuit diagram, in an effort to disseminate the prototype design of the coils to other laboratories. We have included a detailed parts list with the cost for construction of the coils configured for our scanner(supp table 1). These specifics though would need to be adjusted to the precise field strength/bore size/animal the coil was being built for. As for reusability, the copper wire is cemented to the animal skull and this implantable coil should be considered as consumables for the awake mouse experiments, though the PCB parts can be retrieved.</p><disp-quote content-type="editor-comment"><p>(2) In the introduction, the authors state that &quot;Awake mouse fMRI has been well investigated&quot;. I disagree with this statement and others in the manuscript that gives the reader the impression that awake experiments are not a challenging and unresolved approach to fMRI experiments in mice (or rodents). Although there are multiple labs (maybe 15 worldwide) that have conducted awake mouse experiments (with varying degrees of success/thoroughness), we are far from a standardized approach. This is a strength of the current work and should be highlighted as such. I encourage the authors to read the recent systematic review that was published on this topic in Cerebral Cortex by Mandino et al. There are several elements in there that should influence the tone of this piece including awake mouse implementations with the Bruker Cryoprobe, prevalence of surgical preparations, and evaluations of stress.</p></disp-quote><p>Thank you for the comment. We agree with the reviewer that the current stage of awake mouse fMRI studies remains to be improved. And, we have revised the Introduction to highlight the state-of-theart of awake mouse fMRI (Page 4 – line 81-88).</p><disp-quote content-type="editor-comment"><p>(3) The authors also comment on implanted coils reducing animal stress - I don't know where this comment is coming from, as this has not been reported in the literature (to my knowledge) and the authors don't appear to have evaluated stress in their mice.</p></disp-quote><p>Since question 3 and 4 are highly related to the acclimation procedures, we will answer the two questions together.</p><disp-quote content-type="editor-comment"><p>(4) Following on the above point, measures of motion, stress, and more details on the acclimation procedure that was implemented in this study should be included.</p></disp-quote><p>We thank the reviewer to raise the animal training issues.</p><p>During the animal training, we have measured both pupil dynamic and eye motion features from training sessions, of which the detailed procedure is described in Methods (page 7-9 – line 172-236).</p><p>The training procedure is carried out over a total of 5 weeks with four phases of training: i. Holding animal in hands, ii. Head-fixation and pupillometry, iii. Head-fixation and pupillometry with mockMRI acoustic exposure, iv. Head-fixation and pupillometry with Echo-Planar-Imaging (EPI) in the MR scanner. <xref ref-type="table" rid="sa3table1">Author response table 1</xref></p><table-wrap id="sa3table1" position="float"><label>Author response table 1.</label><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="bottom">Training Day of Each Phase</th><th align="left" valign="bottom">Phase 1 (hold in hand)</th><th align="left" valign="bottom">Phase 2 (holder +pupil)</th><th align="left" valign="bottom">Phase 3 (Mock-MRI+pupil)</th><th align="left" valign="bottom">Phase 4 (EPI +pupil)</th></tr></thead><tbody><tr><td align="left" valign="bottom">1</td><td align="left" valign="bottom">5 mins</td><td align="left" valign="bottom">15 mins</td><td align="left" valign="bottom">30 mins</td><td align="left" valign="bottom">60 mins (rs)</td></tr><tr><td align="left" valign="bottom">2</td><td align="left" valign="bottom">10 mins</td><td align="left" valign="bottom">30 mins</td><td align="left" valign="bottom">30 mins</td><td align="left" valign="bottom">60 mins (rs)</td></tr><tr><td align="left" valign="bottom">3</td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">30 mins</td><td align="left" valign="bottom">60 mins (stim)</td></tr><tr><td align="left" valign="bottom">4</td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">30 mins</td><td align="left" valign="bottom">60 mins (stim)</td></tr><tr><td align="left" valign="bottom">5</td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 mins</td><td align="left" valign="bottom"/></tr><tr><td align="left" valign="bottom">6</td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 mins</td><td align="left" valign="bottom"/></tr><tr><td align="left" valign="bottom">7</td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 mins</td><td align="left" valign="bottom"/></tr><tr><td align="left" valign="bottom">8</td><td align="left" valign="bottom"/><td align="left" valign="bottom"/><td align="left" valign="bottom">60 mins</td><td align="left" valign="bottom"/></tr></tbody></table></table-wrap><p>As shown in <xref ref-type="fig" rid="sa3fig2">Author response image 2B</xref>, the spectral power of pupil dynamics (&lt;0.02Hz) and eye movements gradually increased as a function of the training time for head-fixed mice exposed to the mock MRI acoustic environment during phase 3. In phase 4, when head-fixed mice were put into the scanner for the first time, both eye movements and pupil dynamics were initially reduced during scanning but recovered to an acclimated state on Day 2, similar to the level on Day 8 of phase 3. These behavioral outputs would provide an alternative way to monitor the stress levels of the mice.</p><fig id="sa3fig2" position="float"><label>Author response image 2.</label><caption><title>The eye movements (<bold>A</bold>) and power spectra of pupil dynamics (&lt;0.02Hz) (<bold>B</bold>) change during different training phases.</title></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-sa3-fig2-v1.tif"/></fig><p>It should be noted that stress may be related to increased frequency of eye blinking or twitching movements in human subjects(1–3). Whereas, the eyeblink of head-fixed mice has been used for behavioral conditioning to investigate motor learning in normal behaving mice(4–6). Importantly, head-fixed mouse studies have shown that eye movements are significantly reduced compared to the free-moving mice(7). The increased eye movement during acclimation process would indicate an alleviated stress level of the head-fixed mice in our cases. Meanwhile, stress-related pupillary dilation could dominate the pupil dynamics at the early phase of training(8). We have observed a gradually increased pupil dynamic power spectrum at the ultra-slow frequency during phase 3, presenting the alleviated stress-related pupil dilation but recovered pupil dynamics to other factors, including arousal, locomotion, startles, etc. in normal behaving mice. Despite the extensive training procedure of the present work in comparison to the existing awake mouse fMRI studies (training strategies for awake mice fMRI have been reviewed by Mandino et al. to show the overall training duration of existing studies(9)), the stress remains a confounding factor for the brain functional mapping in head-fixed mice. In particular, a recent study(10) shows that the corticosterone concentration in the blood samples of head-fixed mice is significantly reduced on Day 25 following the training but remains higher than in the control mice. In the discussion section, we have discussed the potential issues of stress-related confounding factors for awake mouse fMRI studies (Page 16 – lines 436-458).</p><p>(1) A. Marcos-Ramiro, D. Pizarro-Perez, M. Marron-Romera, D. Gatica-Perez, Automatic blinking detection towards stress discovery. ICMI 2014 - Proceedings of the 2014 International Conference on Multimodal Interaction 307–310 (2014). https://doi.org/10.1145/2663204.2663239/SUPPL_FILE/ICMI1520.MP4.</p><p>(2) M. Haak, S. Bos, S. Panic, L. Rothkrantz, DETECTING STRESS USING EYE BLINKS AND BRAIN ACTIVITY FROM EEG SIGNALS. Lance 21, 76 (2009).</p><p>(3) E. Del Carretto Di Ponti E Sessam, Exploring the impact of Stress and Cognitive Workload on Eye Movements: A Preliminary Study. (2023).</p><p>(4) S. A. Heiney, M. P. Wohl, S. N. Chettih, L. I. Ru olo, J. F. Medina, Cerebellar-dependent expression of motor learning during eyeblink conditioning in head-fixed mice. J Neurosci 34, 14845–14853 (2014).</p><p>(5) S. N. Chettih, S. D. Mcdougle, L. I. Ruffolo, J. F. Medina, Adaptive timing of motor output in the mouse: The role of movement oscillations in eyelid conditioning. Front Integr Neurosci 5, 12996 (2011).</p><p>(6) J. J. Siegel, et al., Trace Eyeblink Conditioning in Mice Is Dependent upon the Dorsal Medial Prefrontal Cortex, Cerebellum, and Amygdala: Behavioral Characterization and Functional Circuitry. eNeuro 2, 51–65 (2015).</p><p>(7) A. F. Meyer, J. O’Keefe, J. Poort, Two Distinct Types of Eye-Head Coupling in Freely Moving Mice. Current Biology 30, 2116-2130.e6 (2020).</p><p>(8) H. Zeng, Y. Jiang, S. Beer-Hammer, X. Yu, Awake Mouse fMRI and Pupillary Recordings in the UltraHigh Magnetic Field. Front Neurosci 16, 886709 (2022).</p><p>(9) F. Mandino, S. Vujic, J. Grandjean, E. M. R. Lake, Where do we stand on fMRI in awake mice? Cereb Cortex 34 (2024).</p><p>(10) K. Juczewski, J. A. Koussa, A. J. Kesner, J. O. Lee, D. M. Lovinger, Stress and behavioral correlates in the head-fixed method: stress measurements, habituation dynamics, locomotion, and motor-skill learning in mice. Scientific Reports 2020 10:1 10, 1–19 (2020).</p><disp-quote content-type="editor-comment"><p>(5) It wasn't clear to me at what times the loop versus &quot;Figure 8&quot; coil was being used, nor how many mice (or how much data) were included in each experiment/plot. There is also no mention of biological sex.</p></disp-quote><p>Thank you for the comment. We have clarified sex and number. The ‘figure 8’ coil was only used as part of development to show the improvement of the coil design for cortical measurements. The detailed information is described in Method (Page 6 – line 127-129 &amp; Page 10 – line 269-270). Additionally animal numbers have been included in the figure captions.</p><disp-quote content-type="editor-comment"><p>(6) Building on the points above, the manuscript overall lacks experimental detail (especially since the format has the results prior to the methods).</p></disp-quote><p>Thank you for the comment. We have modified the manuscript to increase the experimental detail and moved the methods section before the results.</p><disp-quote content-type="editor-comment"><p>(7) An observation is made in the manuscript that there is an appreciable amount of negative BOLD signal. The authors speculate that this may come from astrocyte-mediated BOLD during brain state changes (and cite anesthetized rat and non-human primate experiments). This is very strange to me. First, the negative BOLD signal is not plotted (please do this), further, there are studies in awake mice that measure astrocyte activation eliciting positive BOLD responses (see Takata et al. in Glia, 2017).</p></disp-quote><p>We thank the reviewer to raise the negative BOLD fMRI observation issue. We added a subplot of the negative BOLD signal changes in the revised <xref ref-type="fig" rid="fig4">Figure 4</xref>. This negative BOLD signals across cortical areas could be coupled with brain state changes upon air-puff-induced startle responses. Our future studies are focusing on elucidating the brain-wide activity changes of awake mice with fMRI. We also provide a detailed discussion of the potential mechanism underlying the negative BOLD fMRI signals. First, as reported in the paper (suggested by the reviewer), astrocytic Ca2+ transients coincide with positive BOLD responses in the activated cortical areas, which is aligning with the neurovascular coupling (NVC) mechanism. However, there is emerging evidence to show that astrocytic Ca2+ transients are coupled with both positive and negative BOLD responses in anesthetized rats(11) and awake mice(12). An intriguing observation is that cortex-wide negative BOLD signals coupled with the spontaneous astrocytic Ca2+ transients could co-exist with the positive BOLD signal detected at the activated cortex. Studies have shown that astrocytes are involved in regulating brain state changes(13), in particular, during locomotion(14) and startle responses(15). These brain state-dependent global negative BOLD responses are also related to the arousal changes of both non-human primates(16) and human subjects(17). The established awake mouse fMRI platform with ultra-high spatial resolution will enable the brain-wide activity mapping of the functional nuclei contributing to the brain state changes of head-fixed awake mice in future studies. (Page 17-18 – Line 478-490)</p><p>(11) M. Wang, Y. He, T. J. Sejnowski, X. Yu, Brain-state dependent astrocytic Ca2+ signals are coupled to both positive and negative BOLD-fMRI signals. Proc Natl Acad Sci U S A 115, E1647–E1656 (2018).</p><p>(12) C. Tong, Y. Zou, Y. Xia, W. Li, Z. Liang, Astrocytic calcium signal bidirectionally regulated BOLD-fMRI signals in awake mice in Proc. Intl. Soc. Mag. Reson. Med. 32, (2024).</p><p>(13) K. E. Poskanzer, R. Yuste, Astrocytes regulate cortical state switching in vivo. Proc Natl Acad Sci U S A 113, E2675–E2684 (2016).</p><p>(14) M. Paukert, et al., Norepinephrine controls astroglial responsiveness to local circuit activity. Neuron 82, 1263–1270 (2014).</p><p>(15) R. Srinivasan, et al., Ca2+ signaling in astrocytes from IP3R2−/− mice in brain slices and during startle responses in vivo. Nat Neurosci 18, 708 (2015).</p><p>(16) C. Chang, et al., Tracking brain arousal fluctuations with fMRI. Proc Natl Acad Sci U S A 113, 4518– 4523 (2016).</p><p>(17) B. Setzer, et al., A temporal sequence of thalamic activity unfolds at transitions in behavioral arousal state. Nat Commun 13 (2022).</p><disp-quote content-type="editor-comment"><p><bold>Recommendations for the authors:</bold></p><p><bold>Reviewer #1 (Recommendations For The Authors):</bold></p><p>I really enjoyed this work. The maps shown are among the best-quality maps out there. Here are suggestions to the authors.</p><p>(1) Both the ACA and VRA are rather unexpected. The authors explain these briefly as being part of the associative cortical areas. Both the ACA and VRA are not canonical associative areas (or at least not to us). This warrants a stronger discussion.</p></disp-quote><p>To verify both ACA and VRA as associate areas, we provide the connectivity map projections from the Allen Brain Atlas (seen below). These projections are derived from a Cre-dependent AAV tracing of axonal projections. We have included an explanation of this in the introduction.</p><fig id="sa3fig3" position="float"><label>Author response image 3.</label><caption><title>Representative images are shown indicating connections between the barrel cortex and retrosplenial area from an injection in the barrel cortex (Left panel) as well as the visual cortex and cingulate connection from an injection in the visual cortex (Right panel).</title><p>Images are of connectivity map projections from the Allen Brain Atlas derived from a Cre-dependent AAV tracing of axonal projections (<xref ref-type="bibr" rid="bib94">Oh et al., 2014</xref>)</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-95528-sa3-fig3-v1.tif"/></fig><disp-quote content-type="editor-comment"><p>(2) This is a lot of work. But looking at the figures, this is not obvious. We read in the caption that several hundred trials were used. It would be good to also specify how many mice. It would be clearer to represent this info in the figure as well to support the fact that this is not a trivial acquisition.</p></disp-quote><p>Thank the reviewer to raise the effort issue. We have edited the figure to include this information and included the numbers in the text as well</p><disp-quote content-type="editor-comment"><p>(3) The training protocol is seemingly extensive, but this is only visible by following another reference. Including a description in this work would help the reader make sense of the effort that went into this work.</p></disp-quote><p>We thank the reviewer to raise the training protocol issue. We have more thoroughly discussed the training method used for this study (page 7-9 – line 172-236)</p><disp-quote content-type="editor-comment"><p>(4) I really would love to see that dataset made freely available - this should be the norm.</p></disp-quote><p>The datasets have been uploaded to OpenNeuro</p><p>Whisker (https://doi.org/10.18112/openneuro.ds005496.v1.0.1), Visual (https://doi.org/10.18112/openneuro.ds005497.v1.0.0) and Zenodo:</p><p>SNR Line Profile Data &amp; Data Processing Scripts:</p><p>(https://zenodo.org/doi/10.5281/zenodo.13821455).</p><p>(page 21 – line 573-579)</p><disp-quote content-type="editor-comment"><p><bold>Reviewer #2 (Recommendations For The Authors):</bold></p><p>(1) I'm a little confused about the stimulation paradigm and the effect of it causing an effective 2second TR (which is on the long side) - please elaborate (a figure might be helpful). The paradigm for visual stimulation also seems elaborate, can you please explain the logic and how it was developed?</p></disp-quote><p>Thank you for raising the detailed stimulation paradigm issues. The stimulation paradigm is independent and does not interfere with the setup of the effective 2-second TR. The 2-second TR is based on the usage of 2-segment EPI, each with a TR of 1-second. The application of 2-segment paradigm enables the echo spacing with 0.52 ms with effective image bandwidth with 3858Hz, assuring less image distortion. The stimulation paradigm was defined by an “8s on, 32s off” epoch such to elicit a strong BOLD response and could be used for any reasonable TR duration.</p><p>We have included a figure outlining the stimulation paradigm (<xref ref-type="fig" rid="fig3s1">Figure 3 - Figure Supplement 1</xref>)</p><disp-quote content-type="editor-comment"><p>(2) I had difficulties viewing the movies (on my MAC).</p></disp-quote><p>Thank you for this note. We have re-upload the videos in .mov format</p></body></sub-article></article>