Hello everyone 
I’m trying to perform a diffusion analysis with MRtrix, but I’m having some problems after the “recon-all” step. I need to extract Broca’s and Wernicke’s areas from the T1 parcellated image, but I can’t figure out how to get a mask for these regions. Is there anyone who can explain me how to do this? These regions of interest are necessary to perform “tckgen” command and set them as seeding regions or anything else.
Assuming you know what the index of the relevant region is (I expect you’ll find this in the FreeSurferColorLUT file), you should be able to use mrcalc to do this, for example, to get the ROI for index 1031:
$ mrcalc aparc+aseg.nii.gz 1031 -eq lh-supra-marginal.mif
mrcalc: [100%] uncompressing image "aparc+aseg.nii.gz"
mrcalc: [100%] computing: (aparc+aseg.nii.gz == 1031)
This should produce a mask file in the expected format for use as an ROI in tckgen.