Published March 19, 2019 | Version 1.0.0
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Vascular Territory template and atlases in MNI space

  • 1. Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston MA, USA
  • 2. Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA



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 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 mm3; Repetition Time [TR]: 2510 ms), a 3D-FLAIR (voxel size: 0.9x0.9x0.9 mm3; TR: 5000 ms; TE: 356 ms), and a T2-weighted Turbo Spin Echo (voxel size: 0.5x0.5x2.0 mm3; 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.

Template and territorial map creation

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).

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.


For more details, please see the original publication that utilized the template. If you utilize this template, please also cite

Schirmer, Markus D., et al. "Spatial signature of white matter hyperintensities in stroke patients." Frontiers in neurology 10 (2019): 208.



FLAIR template: caa_flair_in_mni_template_smooth.nii.gz

FLAIR template after brain extraction and intensity normalization: caa_flair_in_mni_template_smooth_brain_intres.nii.gz

T1 template: caa_t1_in_mni_template_smooth.nii.gz 27.7 Mb

T2 template: caa_t2_in_mni_template_smooth.nii.gz 27.7 Mb

Vascular territory map: mni_vascular_territories.nii.gz


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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Additional details

Related works

Is supplement to
10.3389/fneur.2019.00208 (DOI)


ARTEMIS – Assessment of Reserve: Translational Evaluation of Medical Images and Statistics - Prediction models for outcomes of brain health 753896
European Commission