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 I've also fixed the bug by using my own, now-outdated copies of FreeSurfer's MATLAB functions ( https://github.com/epiSurg/EpiSurg/tree/master/FSURF_MATLAB), but I'm hoping the FreeSurfer developers can fix it in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 yaleman@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.groppe@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.