Thanks very much, Yasser. I've also fixed the bug by using my own, now-outdated copies of FreeSurfer's MATLAB functions ( https://github.com/epiSurg/EpiSurg/tree/master/FSURF_MATLAB), but I'm hoping the FreeSurfer developers can fix it in the current releases. much appreciated, -David
On Tue, Dec 27, 2016 at 11:19 AM, Yasser Alemán <yale...@hggm.es> wrote: > Hi David, > > I had the same problem 3 days ago. I have fix it by changing some matlab > scripts located inside freesurfer_root_directory/matlab > > I am sending to you the modified scripts. Please take care and save the > original versions before copying the new ones. > > *Save inside <freesurfer_root_directory>/matlab* > getFacesArea.m > mesh_adjacency.m > SearchProjectionOnPial.m. > > I have also found another bug related to matlab startup.m file. If you > have modified your startup.m file to select by default a working directory > then the lgi computation will fail. When matlab starts it changes the > current directory (*<$SUBJECTS_DIR>/<subjID>/surf*) to the directory > specified in the startup.m file and the scripts are looking for a specified > filename (ie. lh.pial) inside the specified working directory. > > I am sending to you also the modified versions of the scripts with this > bug solved. I have tested in our VMs and everything goes ok. > > *Save inside <freesurfer_root_directory>/bin* > mris_compute_lgi > > *Save inside <freesurfer_root_directory>/matlab* > compute_lgi.m > find_corresponding_center_FSformat.m > make_roi_paths.m > > We have to wait for freesurfer developers to see their opinion. Maybe they > have fixed this already. The original code and changes are commented. > > I hope this can be helpful. > Best regards > Yasser > > > > > > 2016-12-23 16:11 GMT+01:00 David Groppe <david.m.gro...@gmail.com>: > >> >> Dear FreeSurfer Developers, >> I think there is a bug in FreeSurfer's MATLAB code that is used to >> compute the local gyrification index. Specifically, when I run this command: >> >> *recon-all -s PT001 -localGI* >> >> >> I get the following error: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *face 115000 / 118360mesh_outer = vertices: [59182x3 >> double] faces: [118360x3 double] facesOfVertex: [59182x1 >> struct]preparing pial mesh structure ......searching for mesh edges...done >> (171.44 sec).... creating path file for vertex 1 / 59182area file for outer >> ROIs saved at 1In an assignment A(:) = B, the number of elements in A and >> B must be the same.Error in dsearchn (line 79) [d(i),t(i)] = >> min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex = >> dsearchn(vertices,points);Error in reorganize_verticeslist (line 28) >> [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); >> Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist >> (mesh_total, A, mesh_outer, perim, verticeslist, step);* >> >> >> >> >> *>> ERROR: make_roi_paths did not complete successfully!* >> I ran the command in debugging mode and *x* and *yi *are both empty >> variables. >> >> I am using a freshly installed version of the Lion OS X 10.7 (64b Intel) >> version of FreeSurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg; >> freesurfer-Darwin-lion-stable-pub-v5.3.0) and am running on OS 10.11.6 >> using MATLAB version R2015b (8.6.0.267246). The recon-all.log is attached. >> >> Let me know if there is any further information I can provide and thanks >> for producing such a fantastic piece of freeware. >> -David Groppe >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >
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