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