Extract ROI cortical thickness with mri_segstat - Freesurfer

27 Apr 2021


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Dear Freesurfer experts,
My name is Yezhe Lin. I am trying&nbsp;to extract the thickness in an area we found significant in group analysis. However, when we did a t-test on the extracted values, the significance was not obtained. I wonder something could go wrong somewhere and what possibly caused the difference. I attached my scripts for the adjusted pipeline FYI.
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
&nbsp;
# 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
&nbsp;
#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
&nbsp;
#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
&nbsp;tkmedit fsaverage T1.mgz \
&nbsp; -overlay /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii \
&nbsp; -overlay-reg MNI2mm_to_fsaverage.dat \
&nbsp; -fthresh 0.5 \
&nbsp; -surface lh.white -aux-surface rh.white
#register ROI to fsaverage space
cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf \
&nbsp; --mov /mnt/backup2/restore-2021/CBPFreesurfer/FreesurferResults/TP1/FS/mask/MNI152_T1_2mm_rh.thickness.CBPHCagesexeTIVmask.nii \
&nbsp; --reg MNI2mm_to_fsaverage.dat \
--projdist-max 0 1 0.1 \
&nbsp; --interp nearest \
&nbsp; --hemi rh \
&nbsp; --out rh.fsaverage.thickness.CBPHCagesexeTIVmask.mgh
&nbsp;
#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
Hope my questions is clear! Appreciate your kind help and time!
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Best regards,
Yezhe
Yezhe Lin, MD MMed&nbsp; (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin.bee@gmail.com
Twitter: @LinYezhe | LinkedIn&nbsp;| Researchgate
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