You can run mri_vol2surf to sample the ROI onto the surface, eg,
mri_vol2surf --regheader subject --mov yourROI.mgz --projfrac-max 0 1 .1 --hemi lh --o lh.yourROI.mgz
yourROI.mgz should be voxel-for-voxel aligned with the orig.mgz
View your sample with
tksurferfv subject lh inflated -aparc -ov lh.yourROI.mgz -fminmax 0.5 1
You can then get the thickness, area, vol with something like
mri_segstats --i lh.thickness --seg lh.yourROI.mgz --id 1 --sum summary.thickness.dat
When applying it to the area or volume files, make sure to add --accumulate to the command line

On 2/22/2024 8:24 AM, Yakupov, Renat /DZNE wrote:

External Email - Use Caution

Dear Freesurfer users,

I would like to do the following:

- there is an ROI mask image file in the same space as the T1-weighted image

- I would like to use that mask to define the borders of a cortical area

- and then calculate volume and average thickness of the above defined cortical area

I know that I can get a rough estimate of the volume by applying the ROI mask to the the aparc* file and calculating the number of voxels, but what I would really like to do is use the ROI mask to constrain the WM and pial surfaces to the volume inside the ROI and then calculate statistics using the surfaces approach.

I also know that I can combine existing labels, but unfortunately this custom ROI contains parts of various cortical regions, not whole regions.

Any advice would be appreciated!

Best wishes,

Renat.
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