Use mri_label2label specifying the source and target subjects to be the same, a regmethod as surface, and select the --outmask option
On 04/01/2016 11:37 AM, Afzal, Afsana wrote: > Hi Doug, > > I'm trying to map a cortical label onto the surface (i.e. extract a nifti > file for a particular label). So instead of a label.label file, it's a > label.nii that I can load in as an overlay in, say, tksurfer. Is there a way > to do this using freesurfer commands? > > ______________________________ > 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 Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, March 28, 2016 11:16 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol > > 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 > > _______________________________________________ > 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.
