Hi Wanda, You should have this function in $FREESURFER_HOME/matlab, the same way you should have compute_lgi.m and many other matlab functions there. Are you sure that you are looking at the correct location and / or that you didn't delete it?
Marie On Jan 31, 2014, at 11:32 AM, Wanda Truong <wanda.truong...@gmail.com<mailto:wanda.truong...@gmail.com>> wrote: Hi Marie, Yes, I'm using matlab R3013a. In $FREESURFER_HOME/matlab folder I don't have a file called SearchProjectionOnPial.m. Should I create it and paste the updated function? Thanks for your help!! Wanda On 30 January 2014 15:09, Marie Schaer <marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>> wrote: Hi Wanda, I'm not sure to understand your problem. Do you get an error because of using matlab 2013? If yes, I'm not sure to understand whether you modified the SearchProjectionOnPial.m function properly. Can you download the updated function there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html and copy it in the $FREESURFER_HOME/matlab folder (replace the older one with this one). Let me know how it works, Marie On Jan 30, 2014, at 1:50 PM, Wanda Truong <wanda.truong...@gmail.com<mailto:wanda.truong...@gmail.com>> wrote: Hello Marie, I am trying to conduct a local gyrification index analysis, however I am getting this error ERROR: make_roi_paths did not complete successfully! Which is the same as the one posted earlier by someone else: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html I added the "patch": function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); to my $freesurfer_home/matlab directly as a .m file. However, I'm still getting the same error: Error in dsearchn (line 80) [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 Vinas-iMac.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 SFS026 exited with ERRORS at Thu Jan 30 14:26:16 MST 2014 Thanks, Wanda -- Wanda Truong, MSc _______________________________________________ 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. -- Wanda Truong, MSc
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