4-26-2021  extract cortical thickness
 
steps
#make a 3x3x3 ROI using the peak coordinate obtained in group analysis in standard space (MNI152) by fslview

#check ROI location
tkmedit -f /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -overlay MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii -fthresh 0.5
 
# register to fsaverage of the dataset
cd ../fsaverage/surf/ (Freesurfer_Home fsaverage)
fslregister --s fsaverage --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_brain.nii --reg MNI2mm_to_fsaverage.dat
 
#To check results, run:
tkregister2 --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_brain.nii --reg MNI2mm_to_fsaverage.dat --surf orig
 
#view your ROI in the fsaverage subject volume to ensure that it is located where you expect it to be: (two pials clear)
cd $SUBJECTS_DIR/fsaverage/surf
 tkmedit fsaverage T1.mgz \
  -overlay /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii \
  -overlay-reg MNI2mm_to_fsaverage.dat \
  -fthresh 0.5 \
  -surface lh.white -aux-surface rh.white

#register ROI to fsaverage space
cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf \
  --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii \
  --reg MNI2mm_to_fsaverage.dat \
--projdist-max 0 1 0.1 \
  --interp nearest \
  --hemi rh \
  --out rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh
 
#view the ROI registration (on the peak center of significant cluster)

tksurfer fsaverage rh inflated -overlay rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh -fthresh 0.5





# extract values from rh.XXX.CBPvsHC_age_sex_eTIV.10.mgh
mri_segstats --i ../rh.thickness.CBPvsHC_age_sex_eTIV.10.mgh --seg rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh --excludeid 0 --avgwf CBPHC_th_results.dat