which coords are you looking at? They should be the "surface RAS" coords.
On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
>
> 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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