Thanks for posting back on this. I have tried mri_cor2label and have been unable to understand the --labelid id switch. The documentation and experimentation with it shows that it runs from 0-255 only so this labelid is not the one in FreesurferColorLut.txt . Can you clarify this please.

Don

Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

________________________________________ 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: Tuesday, August 05, 2014 6:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] .label files for subcortical structures

You can use mri_cor2label. The output coordinates will be "tkregister-style" RAS, which is probably not useful to you. Check out

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

For how to convert to other coordinate systems doug

On 08/05/2014 11:30 AM, Krieger, Donald N. wrote:

Hi Everyone,

What tool(s) are used to extract the vectors for subcortical labels?

What I need are the RAS coordinates for the cerebellum, basal ganglia, etc.

Is there something for extracting them from aseg.mgz ?

Or is there something for generating a .annot file so that mri_annotation2label may be used?

Or is there some other way?

Thanks.

Don

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