Re: [Freesurfer] Extract coordinates from .mgh file

Use mri_annotation2label to create a label, which will have tkregisterRAS coordinates

On 07/26/2017 08:32 PM, Md. Mamun Al-Amin wrote:

Hi I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. This file is stored in the mri folder. Would you please help me in this regards?

kind regards Mamun

On Thu, Jul 27, 2017 at 9:36 AM, Redwan Maatoug <redwanmaatoug@gmail.com mailto:redwanmaatoug@gmail.com> wrote:

Hi Doug,

Thank you for your reply,
I have used the tool *surf_cluster* to have the MNI coordinates.
Is it a good alternative to *mri_cor2label *?

Thank you very much,
Regards,
Redwan

On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    mri_cor2label with extract the coordinates into a label file. The
    coordinates will be in "tkregisterRAS". What coordinate system
    do you
    want? See

    See
    https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
    <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems>


    On 07/25/2017 07:32 PM, Redwan Maatoug wrote:
    > Hi experts,
    >
    > I just want to know a way to extract the coordinates from a
    ROI mgh file.
    >
    > I know that I can load the file with tksurfer but I have 100
    .mgh
    > files so if I could run a command line to have the
    coordinates in a
    > .txt file or in a .m it would be helpful.
    >
    > Thank you,
    > Redwan
    >
    >
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contains patient information, please contact the Partners
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Kind regards

Md. Mamun Al-Amin

PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072

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