We have a number of subjects on which we have run recon-all to completion. We have a number of ROIs for the parahippocampal gyrus (perirhinal, entorhinal, and parahippocampal cortices) defined in volume space on the original T1-weighted images which are registered well, and I would like to extract cortical thickness estimates from these ROIs.

I have so far been following the page "Cortical Thickness of a Volume-defined ROI" (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness). I am using version 8.1.0. I registered the T1 image to the fsaverage image using:

fslregister --s fsaverage --mov /mnt/d/.../T1_asl_CON_L01.nii --reg T1_asl_CON_L01_to_fsaverage.dat

Which ran without issue. Viewing with the suggested command:

tkregisterfv --mov /mnt/d/../T1_asl_CON_L01.nii --reg T1_asl_CON_L01_to_fsaverage.dat --surf orig

The registration looks pretty good, although the target structures in the parahippocampal gyrus do not perfectly overlap. Continuing with mri_vol2surf:

mri_vol2surf --mov /mnt/d/.../ROIs/T1_asl_CON_L01_L_MTLcROI.mgz --reg T1_asl_CON_L01_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.MTLc.mgh

And then viewing using the new tksurferfv:

tksurferfv fsaverage lh inflated -overlay lh.fsaverage.MTLc.mgh -fthresh 0.5

The ROI appears roughly in the right position, but does not fully overlap the correct gyrus and appears slightly misaligned. Using mri_surf2surf and then writing out the stats with segstats:

mri_surf2surf --s T1_asl_CON_L01 --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh

mri_segstats --seg lh.fsaverage.MTLc.mgh --in lh.thickness.fsaverage.mgh --sum segstats_MTLc_L.txt

The mean thickness is 1mm or less for each of the structures, which does not seem to be correct as manually checking the thickness of parts of the ROIs using measurement tools like ITK-Snap indicates the more expected thickness of ~2.5 - 3.0mm.

I assume this must be due to the slightly misaligned ROI when viewed on the fsaverage brain. I have checked other posts on the mailing list and found the suggestion to specify --dof 12 when running fslregister. However, this made the issue considerably worse with the ROI now located in the brainstem and in entirely the wrong orientation. I'm confused about why this has happened and how to fix either issue.

Thank you, any help greatly appreciated!