The problem is a combination of things in that mri_tessellate writes out a file that read_surf.m cannot read. I have fixed this in our tree. You can get around it by using mri_mc instead of mri_tessellate (same exact command line). mri_mc uses marching cubes.
On 11/05/2018 01:07 PM, Bruss, Joel E wrote:
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Bruce-
Thank you for the reply. I'll try to summarize what I've done (and please see the attached jpeg showing my coordinate examples).
I needed to create a surface of the scalp/skull in order to query vertex coordinates in conjunction with some TMS localization. I ran:
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
I can load lh.seghead into freeview, cursor onto a vertex and note the coordinates. I then load the file into matlab via read_surf. I've since taken care to note that matlab is +1 in vertex number. I've also ran:
mris_curvature -w lh.seghead
as you suggested and reread the file in matlab. Attached are snippets from freeview and matlab showing that when I query lh.pial, I see the correct vertex coordinates in freeview and in matlab. When I do the same thing but use lh.seghead, the coordinates in matlab no longer match the vertex coordinates that I see in freeview., even after running mris_curvature -w.
How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for lh.seghead? If I load that file into matlab with read_surf, why do my coordinates not match what I see in freeview?
-Joel
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Monday, November 5, 2018 11:12:40 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation Hi Joel
Doug is on vacation so I'll try to help. You can use mris_curvature -w ... to recreate the curv files, but I think that is a red herring. Can you summarize what is going on? Have you used mris_info to extract the various transforms from the surface file? Did you fix the off-by-one that Doug noted? cheers Bruce
On Fri, 19 Oct 2018, Bruss, Joel E wrote:
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Doug-
Did you have any other ideas on this? I'm using FreeSurfer 6.0.0,
if that
helps any. I've tried the "mkheadsurf" command on three different
subjects
and all have the same issues. The coordinates I get in matlab are
nowhere
near what I see in Freeview.
-Joel
From: Bruss, Joel E Sent: Tuesday, October 16, 2018 3:53:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
Attached is a screenshot showing what I see in Freeview and what I
see in
Matlab.
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 3:15:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation which coords are you looking at? They should be the "surface RAS"
coords.
On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
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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:
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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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