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Vascular Territory template and atlases in MNI space

Schirmer, Markus D; Giese, Anne-Katrin; Fotiadis, Panagiotis; Etherton, Mark R; Cloonan, Lisa; Viswanathan, Anand; Greenberg, Steven M; Wu, Ona; Rost, Natalia S


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    "language": "eng", 
    "title": "Vascular Territory template and atlases in MNI space", 
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    "notes": "This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 753896 (M.D. Schirmer). This study was supported by the NIH-National Institute of Neurological Disorders and Stroke (K23NS064052, R01NS082285, and R01NS086905), American Heart Association/Bugher Foundation Centers for Stroke Prevention Research, and Deane Institute for Integrative Study of Atrial Fibrillation and Stroke.", 
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        "title": "Assessment of Reserve: Translational Evaluation of Medical Images and Statistics-Prediction models for outcomes of brain health", 
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    "keywords": [
      "Brain", 
      "template", 
      "vascular territories", 
      "anterior", 
      "posterior", 
      "middle", 
      "cerebral artery", 
      "ACA", 
      "PCA", 
      "MCA", 
      "MNI", 
      "T1", 
      "T2", 
      "FLAIR"
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    "publication_date": "2019-03-19", 
    "creators": [
      {
        "orcid": "0000-0001-9561-0239", 
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Schirmer, Markus D"
      }, 
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        "orcid": "0000-0002-8500-2376", 
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Giese, Anne-Katrin"
      }, 
      {
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Fotiadis, Panagiotis"
      }, 
      {
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Etherton, Mark R"
      }, 
      {
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Cloonan, Lisa"
      }, 
      {
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Viswanathan, Anand"
      }, 
      {
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Greenberg, Steven M"
      }, 
      {
        "affiliation": "Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA", 
        "name": "Wu, Ona"
      }, 
      {
        "affiliation": "Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA", 
        "name": "Rost, Natalia S"
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    "description": "<p><strong>Data</strong></p>\n\n<p>Sixteen subjects (mean age (sd): 69.6 (8.2); 37.5% female) were recruited to generate a high-resolution template. The cohort consists of twelve stroke-free, non-demented patients with the sporadic form of cerebral amyloid angiopathy (CAA), and similarly-aged healthy controls (n=4). Each participant underwent high-resolution MRI&nbsp;with a Siemens Magnetom Prisma 3T scanner (using a 32-channel head coil) as part of a separate study. The standardized protocol included a Multiecho T1-weighted (voxel size: 1x1x1 mm<sup>3</sup>; Repetition Time [TR]: 2510 ms), a 3D-FLAIR (voxel size: 0.9x0.9x0.9 mm<sup>3</sup>; TR: 5000 ms; TE: 356 ms), and a T2-weighted Turbo Spin Echo (voxel size: 0.5x0.5x2.0 mm<sup>3</sup>; TR: 7500 ms; TE: 84 ms) sequence. Scans were manually assessed to ensure no gross pathology was present, such as hemorrhage or silent brain infarcts.</p>\n\n<p><strong>Template and territorial map creation</strong></p>\n\n<p>We employed Advanced Normalization Tools (ANTs) for image processing (Avants et al., 2010, 2011) for creating a brain template based on multimodal information using T1, T2 and 3D-FLAIR sequences. After template creation, we smoothed the resulting templates (FSL; Gaussian smoothing, sigma = 1) and registered the resulting templates into MNI space, again using ANTs (Avants et al., 2011).</p>\n\n<p>Vascular territories were outlined on the right hemisphere in the T1-weighted atlas image and contain anatomically validated ACA, MCA, and PCA territories supratentorially. The right hemispheric map was then mirrored onto the left hemisphere to create a full-brain vascular territory map, which was manually assessed and corrected where necessary.</p>\n\n<p>&nbsp;</p>\n\n<p>For more details, please see the original publication that utilized the template. If you utilize this template, please also cite</p>\n\n<p>Schirmer, Markus D., et al. &quot;Spatial signature of white matter hyperintensities in stroke patients.&quot; <em>Frontiers in neurology</em> 10 (2019): 208.</p>\n\n<p><a href=\"https://doi.org/10.3389/fneur.2019.00208\">https://doi.org/10.3389/fneur.2019.00208</a></p>\n\n<p>&nbsp;</p>\n\n<p><strong>Files</strong></p>\n\n<p><strong>FLAIR template</strong>: caa_flair_in_mni_template_smooth.nii.gz<br>\n<br>\n<strong>FLAIR template after brain extraction and intensity normalization</strong>: caa_flair_in_mni_template_smooth_brain_intres.nii.gz<br>\n<br>\n<strong>T1 template</strong>: caa_t1_in_mni_template_smooth.nii.gz 27.7 Mb<br>\n<br>\n<strong>T2 template</strong>: caa_t2_in_mni_template_smooth.nii.gz 27.7 Mb<br>\n<br>\n<strong>Vascular territory map</strong>: mni_vascular_territories.nii.gz</p>"
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