External Email - Use Caution
Dear Gouglas,Thank you for your replay. There is still no ROI name in the summary after adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat.
My updated command is as followed: mri_volcluster --in ./sig.${sigFormat} --thmin ${thvoxel} --sign ${sigsignTemp} --cwpvalthresh 0.05 --minsize 273 --fwhm 6 --no-adjust--sum ${nameout}.cluster.summary --out ${nameout}.cluster.nii.gz --ocn ${nameout}.ocn.nii.gz --labelbase $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label --reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat--mask ${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz
Best, zhiwei
------------------------------------------------------------------------------------------------------------------------------------------------------- Date: Sat, 25 Nov 2023 14:04:08 -0500 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: af2e6147-e3d1-4146-b6f9-b685d6899eb7@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat
On 11/23/2023 2:32 AM, wangzhiwei3233 wrote:
????????External Email - Use Caution
Dear Freesurfer Experts, I did group-level analysis in MNI305 space.? Then I output the summay via command 'mri_volcluster' as follows: /*mri_volcluster --in* ./sig.nii.gz *--thmin* ${thvoxel} *--sign* ${sigsignTemp} *--cwpvalthresh* 0.05 *--minsize* 273 *--fwhm 6* *--no-adjust --sum* ${nameout}.cluster.summary*--out* ${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label *--mask* /mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz/ / / the output is as follows. there are no ROI names in the table. Is it because I missed the option '--reg' in the command line? Which register file shoul I use if I should add it? I can't find the 'register.dat' file in fsaverage folder.
Very appricated if you can help me.
Best, zhiwei
Try adding -seg fsaverage aparc+aseg.mgz
On 1/26/2024 4:59 AM, wangzhiwei3233 wrote:
External Email - Use Caution
Dear Gouglas, Thank you for your replay. There is still no ROI name in the summary after adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat. My updated command is as followed: /mri_volcluster *--in* ./sig.${sigFormat} *--thmin* ${thvoxel} *--sign* ${sigsignTemp} *--cwpvalthresh 0.05 --minsize* 273 *--fwhm* 6 *--no-adjust* *--sum* ${nameout}.cluster.summary *--out* ${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label *--reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat* *--mask *${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz/ // Best, zhiwei
Date: Sat, 25 Nov 2023 14:04:08 -0500 From: "Douglas N. Greve"dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group analysis To:freesurfer@nmr.mgh.harvard.edu Message-ID:af2e6147-e3d1-4146-b6f9-b685d6899eb7@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat
On 11/23/2023 2:32 AM, wangzhiwei3233 wrote:
????????External Email - Use Caution
Dear Freesurfer Experts, I did group-level analysis in MNI305 space.? Then I output the summay via command 'mri_volcluster' as follows: /*mri_volcluster --in* ./sig.nii.gz *--thmin* ${thvoxel} *--sign* ${sigsignTemp} *--cwpvalthresh* 0.05 *--minsize* 273 *--fwhm 6* *--no-adjust --sum* ${nameout}.cluster.summary*--out* ${nameout}.cluster.nii.gz *--ocn* ${nameout}.ocn.nii.gz *--labelbase* $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label *--mask* /mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz/ / / the output is as follows. there are no ROI names in the table. Is it because I missed the option '--reg' in the command line? Which register file shoul I use if I should add it? I can't find the 'register.dat' file in fsaverage folder.
Very appricated if you can help me.
Best, zhiwei
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
wangzhiwei3233