Computational protocol: A semi-automated workflow solution for multimodal neuroimaging: application to patients with traumatic brain injury

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Protocol publication

[…] A high-resolution (1 × 1 × 1 mm3 voxels) single-subject T1-weighted MR brain template [] provided by Montreal Neurological Institute (MNI) was chosen as the common stereotaxic space for matching all structural and functional imaging data to facilitate comparisons across subjects, mapping of 3D ROIs between different spaces, and anatomical labeling. Cortical and subcortical gray matter ROIs from the well-validated automated anatomical labeling (AAL) atlas [] defined on the same MR brain template were used to examine regional physiological parameter values from the functional PET imaging data. Bilateral 3D ROIs were also manually drawn over the centrum semiovale using the ITK-SNAP software ( for subcortical white matter region (SWM), which is not available in the AAL atlas. […]

Pipeline specifications

Software tools AAL, ITK-SNAP
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Injuries