Problem using mri_cor2label

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creating label that is the overlap...

recon-all error using GPU in OS X...

Sophie Wohltjen

7 Nov 2016 7 Nov '16

11:32 a.m.

Hi,

I am trying to create cortical surface labels from several brain masks. All are .mgz files, separated by hemisphere, and aligned to fsaverage.

Here is the command I entered to create the labels:

mri_cor2label --i <filename>.mgz --l <labelname>.label --id 1

When I run this command, I successfully create the label, but I am unable to open the label in tksurfer. I've tried opening both from the GUI menu and from command line, and each time I get the following error:

******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 13245 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... MatrixMultiply: m2 is null!

And then tksurfer closes. I'm not sure why this is happening -- any help would be greatly appreciated!

Thanks, Sophie

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Douglas N Greve

7 Nov 7 Nov

3:20 p.m.

Use the --surf subject hemi option. Run it with --help to get an example

On 11/07/2016 11:32 AM, Sophie Wohltjen wrote:

...

Hi,

I am trying to create cortical surface labels from several brain masks. All are .mgz files, separated by hemisphere, and aligned to fsaverage.

Here is the command I entered to create the labels:

mri_cor2label --i <filename>.mgz --l <labelname>.label --id 1

When I run this command, I successfully create the label, but I am unable to open the label in tksurfer. I've tried opening both from the GUI menu and from command line, and each time I get the following error:

--

******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 13245 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... MatrixMultiply: m2 is null!

--

And then tksurfer closes. I'm not sure why this is happening -- any help would be greatly appreciated!

Thanks, Sophie

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/

Sophie Wohltjen

17 Nov 17 Nov

11:02 a.m.

Hi,

I'm still having this issue. I'd appreciate any insight you might have!

Thanks, Sophie

On Mon, Nov 7, 2016 at 11:32 AM Sophie Wohltjen sophiewohltjen@gmail.com wrote:

...

Hi,

I am trying to create cortical surface labels from several brain masks. All are .mgz files, separated by hemisphere, and aligned to fsaverage.

Here is the command I entered to create the labels:

mri_cor2label --i <filename>.mgz --l <labelname>.label --id 1

When I run this command, I successfully create the label, but I am unable to open the label in tksurfer. I've tried opening both from the GUI menu and from command line, and each time I get the following error:

--

******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 13245 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... MatrixMultiply: m2 is null!

--

And then tksurfer closes. I'm not sure why this is happening -- any help would be greatly appreciated!

Thanks, Sophie

Douglas N Greve

1:56 p.m.

Add --surf subjectname hemi to create a surface-based label

On 11/17/2016 11:02 AM, Sophie Wohltjen wrote:

...

Hi,

I'm still having this issue. I'd appreciate any insight you might have!

Thanks, Sophie

On Mon, Nov 7, 2016 at 11:32 AM Sophie Wohltjen <sophiewohltjen@gmail.com mailto:sophiewohltjen@gmail.com> wrote:

Hi,

I am trying to create cortical surface labels from several brain
masks. All are .mgz files, separated by hemisphere, and aligned to
fsaverage.

Here is the command I entered to create the labels:

mri_cor2label --i <filename>.mgz --l <labelname>.label --id 1

When I run this command, I successfully create the label, but I am
unable to open the label in tksurfer. I've tried opening both from
the GUI menu and from command line, and each time I get the
following error:

--

********************      0 nonzero vertices found
********************
label stat field identically zero - setting to 1
13245 unassigned vertices in label - building spatial LUT...
assigning vertex numbers to label...
MatrixMultiply: m2 is null!

--

And then tksurfer closes. I'm not sure why this is happening --
any help would be greatly appreciated!

Thanks,
Sophie

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Douglas N Greve
Sophie Wohltjen