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Dear Freesurfer experts,
My name is Yezhe Lin. I am trying 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 # 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
Hope my questions is clear! Appreciate your kind help and time!
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Best regards,
Yezhe
Yezhe Lin, MD MMed (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin.bee@gmail.com
Twitter: @LinYezhe | LinkedIn | Researchgate