Significant in group analysis of what? The commands look ok
On 4/27/2021 9:18 AM, LIN, Yezhe wrote:
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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!
------------------
Best regards,
Yezhe
Yezhe Lin, MD MMed (she/her/hers)
Postdoctoral Associate, Department of Psychiatry
University of Rochester Medical Center
yezhe.lin....@gmail.com
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