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"<dgr...@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-b685d6899...@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
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