Try adding -seg fsaverage aparc+aseg.mgz
On 1/26/2024 4:59 AM, wangzhiwei3233 wrote:
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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:
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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
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