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:
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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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