Hi FreeSurfer experts,
My goal is to extract cortical thickness of several ROIs, which are in volume space. I am following instructions from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
My ROIs and T1 image are in the form of binary mask and are already in same standard space (MNIT1.nii). So following the instructions, I am able to perform until step 3 (I created registration file X.dat using fslregister command to register MNIT1.nii with fslaverage).
After that I am using this command: tksurfer fsaverage lh inflated -overlay lh.fsaverage.ROI5.mgh -fthresh 0.5
to make sure that the ROI in surface format is at correct place. But after I run this command I do not see the region anywhere on surface. I tried to view it using FreeView also, its giving me attached image. From FreeView it looks like the ROI is now a brain mask and is all over the brain with a constant value everywhere. I am not sure why this is happening.
Next, I have 26 ROIs, 12 on left hemisphere, 12 on right hemisphere and 2 in the midline. Somehow, 11/12 ROIs on left hemisphere and 2 ROIs in the midline are working fine when I view those in tksurfer or FreeView but rest all are showing me value of 1 all over the brain.
For left hemisphere and midline ROIs, I am using exactly same steps as mentioned in the instructions but for right hemisphere, I just replaced 'lh' with 'rh' in step 3.
Any help would be really appreciated.
