Sorry, what are you trying to do? mri_label2vol maps a label (ie, ROI, segmentataion, annotation) into a volume space. Do you just want to map the surface overlay (fmcpr.sm4.fsaverage.lh.b0dc.nii) into the volume space? If so, use mri_surf2vol. You can use the version below (using method1 from the help)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol On 03/28/2016 10:13 AM, Afzal, Afsana 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 is27307x1x6. > This dimension mismatch is causing issues in our gPPI pipeline. > > How can I generate a .nii output file with the27307x1x6 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 > ------------------------------------------------------------------------ > *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 is27307x1x6. > This dimension mismatch is causing issues in our gPPI pipeline. > > How can I generate a .nii output file with the27307x1x6 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
