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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [AAFZAL@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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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