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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
