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:
External Email - Use Caution
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-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 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:
>
> 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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