Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else.
-- Natalia Sanchez
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