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Doug-


I had time to play around with this, substituted the mri_mc command and.... success!   Thank you so much for resolving this issue.  Is this something that will be incorporated into the next release or will I have to remember to run this command for any other surfaces that I create?


-Joel

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: Thursday, November 8, 2018 9:26:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation
 
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:
>
>         External Email - Use Caution
>
> 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:
>
> >
> >         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-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:
> > >
> > >         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-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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