I want to measure the cortical thickness for an ROI.
I have been following the instructions in http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
my ROI is the PFC (pre frontal cortex) I made the ROI in AFNI and converted it to NIFTI format
I confirmed that the ROI is in the expected place with :
tkmedit -f T1.mgz -overlay MJ0015_PFC_ROI.nii -fthresh 0.5 i have attached a picture "PFC_ROI.jpg"
then i rane fslregister to register the ROI - anatomical voul to the FSaverage subject
fslregister --s fsavreage --mov /Studies/MJMRI/MJ0015/freesurfer/mri/T1.mgz --reg T1_to_fsaverage.dat
i viewed the result with
tkmedit fsaverage T1.mgz -overlay /Studies/MJMRI/MJ0015/freesurfer/mri/MJ0015_PFC_ROI.nii -overlay-reg T1_to_fsaverage.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white
i have attached a snapshot "aligned.jpg" the ROI is not aligned well. it has been rotated 90 degrees, and is in the right side of the brain, instead of the prefrontal location.
how can I fix this? THanks Jon
