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
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------------------------------------------------
> > > Notice: This UI Health Care e-mail (including attachments) is covered
> > > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and
> > > is intended only for the use of the individual or entity to which it
> > > is addressed, and may contain information that is privileged,
> > > confidential, and exempt from disclosure under applicable law. If you
> > > are not the intended recipient, any dissemination, distribution or
> > > copying of this communication is strictly prohibited. If you have
> > > received this communication in error, please notify the sender
> > > immediately and delete or destroy all copies of the original message
> > > and attachments thereto. Email sent to or from UI Health Care may be
> > > retained as required by law or regulation. Thank you.
> > > ------------------------------------------------------------------------
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ------------------------------------------------------------------------
> > Notice: This UI Health Care e-mail (including attachments) is covered
> > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and
> > is intended only for the use of the individual or entity to which it
> > is addressed, and may contain information that is privileged,
> > confidential, and exempt from disclosure under applicable law. If you
> > are not the intended recipient, any dissemination, distribution or
> > copying of this communication is strictly prohibited. If you have
> > received this communication in error, please notify the sender
> > immediately and delete or destroy all copies of the original message
> > and attachments thereto. Email sent to or from UI Health Care may be
> > retained as required by law or regulation. Thank you.
> > ------------------------------------------------------------------------
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ____________________________________________________________________________
> Notice: This UI Health Care e-mail (including attachments) is covered by the
> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended
> only for the use of the individual or entity to which it is addressed, and
> may contain information that is privileged, confidential, and exempt from
> disclosure under applicable law. If you are not the intended recipient, any
> dissemination, distribution or copying of this communication is strictly
> prohibited. If you have received this communication in error, please notify
> the sender immediately and delete or destroy all copies of the original
> message and attachments thereto. Email sent to or from UI Health Care may be
> retained as required by law or regulation. Thank you.
>
> ____________________________________________________________________________
>
>


Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you.