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.87@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

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