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

---

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.

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

---

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 greve@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

That works perfectly, thank you!

______________________________ 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: Friday, April 01, 2016 11:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatch in dimensions using mri_label2vol

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-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

---

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 greve@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 greve@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