Dear all,

I solved the problem posted earlier that was similar to a problem before.
It was a matlab version problem.

Conclusion :

if recon-all -localGI command is stopping at make_roi_paths and you use matlab 2013

1. either switch to a older matlab version
or
2. follow the instructions from webpage
http://freesurfer.net/fswiki/ReleaseNotes?highlight=%28%28LGI%29%29

and change the  SearchProjectionOnPial.m file.

Freesurfer webpage information:

find this line:

< for t=1:step:size(perim,2)

and change to:

> si=max(size(perim));
> for t=1:step:si

After this it worked for me also.

Best regards,
Georgiana

Am 13.11.2015 um 15:37 schrieb Oana Georgiana Rus:
Dear all,

when I run the recon-all -localGI command.
I encaunter the same problem as previous described by Meenal (see email below).
It seems that the processing stops at the matlab command make_roi_paths.

Does anybody encaunter a similar problem and somehow solved it?

Thanks in advance.

Georgiana

Am 04.11.2015 um 17:25 schrieb Dr Meenal Yadav:
Hi List,
I am getting the following error when running recon-all ­lgi for local gyrification index.
I have changed the script in matlab as we are using matlab 2013b as mentioned in the previous thread.
I am attaching the script.
Please let me know what else to do.
Thanks Regards
Meenal Budhiraja
PhD student
Karolinska Institute
Stockholm,Sweden.



preparing pial mesh structure ...
...searching for mesh edges...done (349.20 sec).
... creating path file for vertex 1 / 66330
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!


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-- 
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971


_______________________________________________
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.


-- 
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971