I'll take a stab.
On Mon, Mar 28, 2016 at 10:13 AM, Afzal, Afsana AAFZAL@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-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 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
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