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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@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-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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > 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. 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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. 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