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<meta name="DC.Title" content="Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways" />
<meta name="DC.Identifier" content="10.3174/ajnr.A6542" />
<meta name="DC.Date" content="2020-05-01" />
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<meta name="DC.Description" content="BACKGROUND AND PURPOSE: The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.

MATERIALS AND METHODS: After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside k -space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.

RESULTS: The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).

CONCLUSIONS: The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.

FGATIR
:   fast gray matter acquisition T1 inversion recovery" />
<meta name="DC.Contributor" content="T.M. Shepherd" />
<meta name="DC.Contributor" content="B. Ades-Aron" />
<meta name="DC.Contributor" content="M. Bruno" />
<meta name="DC.Contributor" content="H.M. Schambra" />
<meta name="DC.Contributor" content="M.J. Hoch" />
<meta name="article:published_time" content="2020-05-01" />
<meta name="article:section" content="Adult Brain" />
<meta name="citation_title" content="Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways" />
<meta name="citation_abstract" lang="en" content="&lt;h3&gt;BACKGROUND AND PURPOSE:&lt;/h3&gt;
&lt;p&gt;The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.&lt;/p&gt;&lt;h3&gt;MATERIALS AND METHODS:&lt;/h3&gt;
&lt;p&gt;After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside &lt;i&gt;k&lt;/i&gt;-space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.&lt;/p&gt;&lt;h3&gt;RESULTS:&lt;/h3&gt;
&lt;p&gt;The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).&lt;/p&gt;&lt;h3&gt;CONCLUSIONS:&lt;/h3&gt;
&lt;p&gt;The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.&lt;/p&gt;" />
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<meta name="citation_author" content="B. Ades-Aron" />
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<meta name="citation_author_institution" content="bElectrical and Computer Engineering (B.A.-A.)" />
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<meta name="twitter:title" content="Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways" />
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<meta name="twitter:image" content="http://ajnr-stage2.stage.highwire.org/sites/default/files/highwire/ajnr/41/5.cover-source.jpg" />
<meta name="twitter:description" content="BACKGROUND AND PURPOSE: The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.

MATERIALS AND METHODS: After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside k -space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.

RESULTS: The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).

CONCLUSIONS: The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.

FGATIR
:   fast gray matter acquisition T1 inversion recovery" />
<meta name="og-title" property="og:title" content="Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways" />
<meta name="og-url" property="og:url" content="http://ajnr-stage2.stage.highwire.org/content/41/5/777" />
<meta name="og-site-name" property="og:site_name" content="American Journal of Neuroradiology" />
<meta name="og-description" property="og:description" content="BACKGROUND AND PURPOSE: The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.

MATERIALS AND METHODS: After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside k -space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.

RESULTS: The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).

CONCLUSIONS: The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.

FGATIR
:   fast gray matter acquisition T1 inversion recovery" />
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      <div class="highwire-cite-overline"><span  class="highwire-cite-metadata-article-type highwire-cite-metadata">Research Article</span><span class="separator-pipe"></span><span  class="highwire-cite-metadata-art-cat highwire-cite-metadata"><span class="wrapper">Adult Brain</span></span></div>
  
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      <h1 class="highwire-cite-title" id="page-title">Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways</h1>  
    	<div class="highwire-cite-authors"><span  class="highwire-citation-authors"><span class="highwire-citation-author first" data-delta="0">T.M. Shepherd</span>, <span class="highwire-citation-author" data-delta="1">B. Ades-Aron</span>, <span class="highwire-citation-author" data-delta="2">M. Bruno</span>, <span class="highwire-citation-author" data-delta="3">H.M. Schambra</span> and <span class="highwire-citation-author" data-delta="4">M.J. Hoch</span></span></div>
  
    	<div class="highwire-cite-metadata"><span  class="highwire-cite-metadata-journal highwire-cite-metadata">American Journal of Neuroradiology </span><span  class="highwire-cite-metadata-date highwire-cite-metadata">May 2020,  </span><span  class="highwire-cite-metadata-volume highwire-cite-metadata">41 </span><span  class="highwire-cite-metadata-issue highwire-cite-metadata">(5) </span><span  class="highwire-cite-metadata-pages highwire-cite-metadata">777-784; </span><span  class="highwire-cite-metadata-doi highwire-cite-metadata">DOI: https://doi.org/10.3174/ajnr.A6542 </span></div>
  
  
  
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<div id="hw-article-author-popups-top-node-75151--61831884669" style="display: none;"><div class="author-tooltip-0"><div class="author-tooltip-name">T.M. Shepherd </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span>From the Departments of Radiology (T.M.S., B.A.-A., M.B.)</div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&amp;gs_type=author&amp;author%5B0%5D=T.M.%2BShepherd%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Shepherd%20T&amp;link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link"><a href="/search/author1%3AT.M.%2BShepherd%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li><li class="author-orcid-link last"><a href="https://orcid.org/0000-0003-0232-1636" target="_blank" class="" data-icon-position="" data-hide-link-title="0">ORCID record for T.M. Shepherd</a></li></ul></div><div class="author-tooltip-1"><div class="author-tooltip-name">B. Ades-Aron </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span>From the Departments of Radiology (T.M.S., B.A.-A., M.B.)</div><div class='author-affiliation'><span class='nlm-sup'>b</span>Electrical and Computer Engineering (B.A.-A.)</div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&amp;gs_type=author&amp;author%5B0%5D=B.%2BAdes-Aron%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Ades-Aron%20B&amp;link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link"><a href="/search/author1%3AB.%2BAdes-Aron%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li><li class="author-orcid-link last"><a href="https://orcid.org/0000-0001-5077-3341" target="_blank" class="" data-icon-position="" data-hide-link-title="0">ORCID record for B. Ades-Aron</a></li></ul></div><div class="author-tooltip-2"><div class="author-tooltip-name">M. Bruno </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>a</span>From the Departments of Radiology (T.M.S., B.A.-A., M.B.)</div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&amp;gs_type=author&amp;author%5B0%5D=M.%2BBruno%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Bruno%20M&amp;link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link"><a href="/search/author1%3AM.%2BBruno%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li><li class="author-orcid-link last"><a href="https://orcid.org/0000-0003-1625-0293" target="_blank" class="" data-icon-position="" data-hide-link-title="0">ORCID record for M. Bruno</a></li></ul></div><div class="author-tooltip-3"><div class="author-tooltip-name">H.M. Schambra </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>c</span>Neurology (H.M.S.), New York University, New York, New York</div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&amp;gs_type=author&amp;author%5B0%5D=H.M.%2BSchambra%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Schambra%20H&amp;link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link"><a href="/search/author1%3AH.M.%2BSchambra%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li><li class="author-orcid-link last"><a href="https://orcid.org/0000-0002-1886-2288" target="_blank" class="" data-icon-position="" data-hide-link-title="0">ORCID record for H.M. Schambra</a></li></ul></div><div class="author-tooltip-4"><div class="author-tooltip-name">M.J. Hoch </div><div class="author-tooltip-affiliation"><span class="author-tooltip-text"><div class='author-affiliation'><span class='nlm-sup'>d</span>Department of Radiology (M.J.H.), University of Pennsylvania, Philadelphia, Pennsylvania.</div></span></div><ul class="author-tooltip-find-more"><li class="author-tooltip-gs-link first"><a href="/lookup/google-scholar?link_type=googlescholar&amp;gs_type=author&amp;author%5B0%5D=M.J.%2BHoch%2B" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on Google Scholar</a></li><li class="author-tooltip-pubmed-link"><a href="/lookup/external-ref?access_num=Hoch%20M&amp;link_type=AUTHORSEARCH" target="_blank" class="" data-icon-position="" data-hide-link-title="0">Find this author on PubMed</a></li><li class="author-site-search-link"><a href="/search/author1%3AM.J.%2BHoch%2B" rel="nofollow" class="" data-icon-position="" data-hide-link-title="0">Search for this author on this site</a></li><li class="author-orcid-link last"><a href="https://orcid.org/0000-0002-3435-4662" target="_blank" class="" data-icon-position="" data-hide-link-title="0">ORCID record for M.J. 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