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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@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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