Sorry for the delay. That page is not what you should used to do this. Instead, map you volume labels onto the surface, eg, with mri_vol2surf --mov yourvolumelabel.mgz --regheader subjectname --hemi lh --projfrac-max 0 1 .1 --o label/lh.yourlabel.mgz You may want to embed a color table. If so, create a colortable like $FREESURFER/FreeSurferColor.lut The index (first number) should match that in your label. Then mri_convert --ctab your.ctab lh.yourlabel.mgz lh.yourlabel.mgz Load this onto the surface tksurferfv subjectname lh inflated -annot yourlabel.mgz If this looks ok, then you can run mri_segstats --annot subjectname lh yourlabel.mgz --excludeid 0 --sum sum.lh.dat
On 8/7/2025 9:52 AM, Rowan Lawrence wrote:
External Email - Use Caution
Hello FreeSurfers,
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 https://secure-web.cisco.com/1DVU7ZoSo7uvfZJSPChJydu5jwQ_zDu8idGFGJ4xbpLsX8KXYwscLr8W7NwGDxAXxKXW86Mw1cD9kIZslldRuVRIVMeQq3W6GMb5SGCvq8OikujXoOH7Tj-AsLfGA270_Jefqsi91-GJp28U5ebVtvtFxYAbgaK2jiMKavUpLDZgprhEePJa05Unq-xjy3mA3_tgIxlz8juKEaQeXcpk-hDHR-5XmM5IzYs2QhEWHvFuGv6fEOLeyseQCGx00xgPsNWoDW63Qq283pJcAsfI9GORPOPaY2FclGndY5Pz5ecuoQ3SOc3x5rydG9vFvadoo1_PuuGTkanP60d-sgAEWkA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness). 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!
Best wishes, Rowan
~ /GTA/PhD Candidate/ /School of Health Sciences/ /Booth St. East, 4.034 - M13 9SS/
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