Hi all, To follow-up on this issue if anyone else has the same problem, you need to modify one of the LGI functions as described in the release notes (http://freesurfer.net/fswiki/ReleaseNotes):
* LGI: issue when using Matlab 2013. the fix is to edit the file $FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these changes: find this line: < for t=1:step:size(perim,2) and change to: > si=max(size(perim)); > for t=1:step:si Best, Marie On 05 Mar 2016, at 11:10, Marie Schaer <marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>> wrote: Hi Ankita, Did you get this error with only one subject, or with several different subjects? Have you checked your pial surface with freeview or tkmedit? No issue there? If your pial surfaces are fine and you get the issue for all the subjects you tried, send me a sample of pial surface + T1.mgz so that I can have a look. Best, Marie On 05 Mar 2016, at 09:00, Ankita Chatterjee <acha...@gmail.com<mailto:acha...@gmail.com>> wrote: I ran the process, but it came up with an error that says "error: make_roi_paths did not complete successfully." I have attached the recon-all.log so hopefully someone can take a look at it and give me some pointers on what I can do to fix this. Thank you again! On Sat, Mar 5, 2016 at 8:35 AM, Ankita Chatterjee <acha...@gmail.com<mailto:acha...@gmail.com>> wrote: That's perfect. I think that solved the issue. It was not referencing the matlab files from freesurfer I guess. Thank you so much! It seems to be processing now! Thanks! Ankita On Sat, Mar 5, 2016 at 8:05 AM, Ankita Chatterjee <acha...@gmail.com<mailto:acha...@gmail.com>> wrote: Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH on Matlab? I am not very familiar with linux... Thanks! Ankita <recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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 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.
