I'll take a stab. On Mon, Mar 28, 2016 at 10:13 AM, Afzal, Afsana <aaf...@mgh.harvard.edu> wrote: > Hi, Just wanted to follow up on the issue below regarding the dimension of > the mri_label2vol output. > > > Hi, > > I'm using mri_label2vol with the parameters below but the output .nii volume > has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension > mismatch is causing issues in our gPPI pipeline. > > How can I generate a .nii output file with the 27307x1x6 dimension?
I don't think that is what you want. That NIFTI has the following dimensions: vertices, N/A, timepoints. It doesn't make sense to make a nifti label file (typically a volume) out of surface data. What volume are you using in your gPPI pipeline? You will probably want a 3d volume nifti file not one with surface data in it. hth d > > mri_label2vol > --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from > preproc step) > --label label_name.label > --o label_name.nii > --identity > > Thanks, > > Afsana > ______________________________ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana > [aaf...@mgh.harvard.edu] > Sent: Wednesday, March 23, 2016 2:44 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Mismatch in dimensions using mri_label2vol > > Hi, > > I'm using mri_label2vol with the parameters below but the output .nii volume > has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension > mismatch is causing issues in our gPPI pipeline. > > How can I generate a .nii output file with the 27307x1x6 dimension? > > mri_label2vol > --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from > preproc step) > --label label_name.label > --o label_name.nii > --identity > > Thanks, > > Afsana > > ______________________________ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
