Dear FS experts, I had no answer to my question below (log was attached in my previous mail) The error repeated in different subjects and I do not know how to overcome. Can anyone give me some help?
Angela
Hi all, I had an error message while running LGI recon I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with the Image processing toolbox
Any help is welcome. Thank you! Angela
the error is:
mesh_outer =
vertices: [61278x3 double] faces: [122552x3 double] facesOfVertex: [61278x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (315.30 sec). ... creating path file for vertex 1 / 61278 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix.
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! Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ 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.
Hi Angela,
Have you tried that: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?
You can look also in the release notes (http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using Matlab 2013.
The issue will be corrected in the next FreeSurfer release.
Let mw know if it doesn't work,
Marie
On Jul 19, 2014, at 1:56 AM, angela.favaro@unipd.it wrote:
Dear FS experts, I had no answer to my question below (log was attached in my previous mail) The error repeated in different subjects and I do not know how to overcome. Can anyone give me some help?
Angela
Hi all, I had an error message while running LGI recon I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with the Image processing toolbox
Any help is welcome. Thank you! Angela
the error is:
mesh_outer =
vertices: [61278x3 double] faces: [122552x3 double]facesOfVertex: [61278x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (315.30 sec). ... creating path file for vertex 1 / 61278 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix.
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! Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thank you Marie!
Hi Angela,
Have you tried that: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html ?
You can look also in the release notes (http://freesurfer.net/fswiki/ReleaseNotes), under LGI issue when using Matlab 2013.
The issue will be corrected in the next FreeSurfer release.
Let mw know if it doesn't work,
Marie
On Jul 19, 2014, at 1:56 AM, angela.favaro@unipd.it wrote:
Dear FS experts, I had no answer to my question below (log was attached in my previous mail) The error repeated in different subjects and I do not know how to overcome. Can anyone give me some help?
Angela
Hi all, I had an error message while running LGI recon I am using Freesurfer 5.3 with a MacOS lion 10.7.5 and Matlab 2013b with the Image processing toolbox
Any help is welcome. Thank you! Angela
the error is:
mesh_outer =
vertices: [61278x3 double] faces: [122552x3 double]facesOfVertex: [61278x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (315.30 sec). ... creating path file for vertex 1 / 61278 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix.
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! Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
recon-all -s subj001 exited with ERRORS at Tue Jul 15 10:23:17 CEST 2014
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ 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.
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
freesurfer@nmr.mgh.harvard.edu
-
angela.favaro＠unipd.it -
Marie Schaer