Hi there

I am new to Freesurfer and I would like some help with best practices for exporting binary GM, WM and CSF masks.

I have run recon-all (FS v7.1) on some T1w images. I would now like to create binary GM, WM and CSF masks from the recon-all results. I have an existing adapted script that uses AFNI’s 3dcalc to match certain label values in aparc+aseg.mgz and output binary masks (I have since realized I can also use mri_binarize for that), see below for the exact label values that are matched and added together per tissue segmentation. However, I have also seen the output files such as brainmask.mgz, ribbon.mgz, wm.mgz; so I am uncertain about what the standard practices are for creating binary masks for GM, WM and CSF from freesurfer’s output.

I’ve searched a bit on the mailing list and found two similar questions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46545.html and https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11365.html. However, these suggest different approaches (e.g. inverting WM and VCSF to get GM, vs matching several structures and adding them together), and I am unsure whether these will end up covering the same voxels.

So, my main question is: is there a standard best practice for generating binary masks for GM, WM and CSF, i.e. which labels should be included or excluded? Or which standard outputs of freesurfer should be used?

Additionally I would also like to get a binary mask of the amygdala and the Brodmann areas 4a, 4p and 6. The amygdala seems to work fine. For the motor areas, I have tried my standard route of matching the label values (404, 405, 406 respectively) in aparc+aseg.mgz, but this doesn’t seem to yield any matches, i.e. all voxels in the resulting mask image have value zero. My second question: can you perhaps think of a reason for this error? And question 2, part 2: I assume BA 4a, 4p and 6 are all bilateral, since I didn’t see them being specified as LH or RH, is there a quick way to get only the LH?

Best regards,

Stephan Heunis

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GM, WM and CSF labels used in current script:

# Grey matter:
#   Subcortical nuclei:
#   - 10: Left-Thalamus-Proper
#   - 11: Left-Caudate
#   - 12: Left-Putamen
#   - 49: Right-Thalamus-Proper
#   - 50: Right-Caudate
#   - 51: Right-Putamen
#   Cerebellum:
#   - 8: Left-Cerebellum-Cortex
#   - 47: Right-Cerebellum-Cortex
#   Hippocampus and amygdala
#   - 17: Left-Hippocampus
#   - 18: Left-Amygdala
#   - 53: Right-Hippocampus
#   - 54: Right-Amygdala
#   Cortical ribbon:
#   - within(a,1000,3000): ctx-lh-[all], ctx-rh-[all]

# White Matter:
#   - 2: Left-Cerebral-White-Matter
#   - 7: Left-Cerebellum-White-Matter
#   - 41: Right-Cerebral-White-Matter
#   - 46: Right-Cerebellum-White-Matter
#   - 251: CC_Posterior
#   - 252: CC_Mid_Posterior
#   - 253: CC_Central
#   - 254: CC_Mid_Anterior
#   - 255: CC_Anterior

# CSF:
#   - 4: Left-Lateral-Ventricle
#   - 14: 3rd-Ventricle
#   - 43: Right-Lateral-Ventricle