External Email - Use Caution
I couldn't remember if it's 1+ or 1-. Either way, either direction give
similar coordinates that don't match up to what I can see in FreeView.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu>
Sent: Tuesday, October 16, 2018 1:48:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] Nonsensical Vertex Coordinates, please
help with interpretation
When you look at the vertex in matlab, are you correctly accounting for
the fact that FreeView uses 0-based indexing and matlab uses 1-based?
Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be
using 234740 in matlab below
On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I'm trying to make a surface file from a subject's head and to map
> coordinates to that surface. If I run:
>
>
> mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol
> $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2
> 20 --nhitsmin 2
>
> mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255
> $SUBJECTS_DIR/$sub/surf/lh.seghead
>
> and then load lh.seghead in FreeView, it looks as I would expect.
> Clicking anywhere near a vertex gives the typical output, showing the
> closest vertex. All fine and well. However, if I load the file in Matlab:
>
>
> vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
>
>
> my values are nothing near what I'm seeing in Freeview. For example,
> FreeView reports:
>
>
> vertex 234741 [-78.50,14.50,26.50]
>
>
> read_surf reports:
>
>
> vertex 234740 0168.9800000000000
>
> Of note, an error log tells me that:
>
> MRISreadNewCurvature: incompatible vertex number in file
> $SUBJECTS_DIR/$sub/surf/lh.curv
>
>
> How do I edit, update or create a curv file to play with the new
> surface file, or what can I do to get sensical surface coordinates
> from this data?
>
> Thanks,
> Joel
>
>
>
>
>
>
>
>
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Notice: This UI Health Care e-mail (including attachments) is covered by the
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contain information that is privileged, confidential, and exempt from
disclosure under applicable law. If you are not the intended recipient, any
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prohibited. If you have received this communication in error, please notify the
sender immediately and delete or destroy all copies of the original message and
attachments thereto. Email sent to or from UI Health Care may be retained as
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