Hello Freesurfer users/developers, I want to run recon-all localGI on a subject who has been processed with Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on “make_roi_paths”. There error can be found at the end of this email. I looked at the 5.3 release notes and found the that one issue with localGI was fixed by substituting a line of code. The current SearchProjectionOnPial.m that I am using uses this fix.
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
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/working/ABCD/FS/NDAR_INV021N0FLH/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_58433_.m');
exit
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>> loading datas ...
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done ( 0.04 sec)
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done ( 0.02 sec)
preparing outer mesh structure ...
face 5000 / 130188
face 10000 / 130188
face 15000 / 130188
face 20000 / 130188
face 25000 / 130188
face 30000 / 130188
face 35000 / 130188
face 40000 / 130188
face 45000 / 130188
face 50000 / 130188
face 55000 / 130188
face 60000 / 130188
face 65000 / 130188
face 70000 / 130188
face 75000 / 130188
face 80000 / 130188
face 85000 / 130188
face 90000 / 130188
face 95000 / 130188
face 100000 / 130188
face 105000 / 130188
face 110000 / 130188
face 115000 / 130188
face 120000 / 130188
face 125000 / 130188
face 130000 / 130188
mesh_outer =
vertices: [65096x3 double]
faces: [130188x3 double]
facesOfVertex: [65096x1 struct]
preparing pial mesh structure ...
...searching for mesh edges...done (134.42 sec).
... creating path file for vertex 1 / 65096
area file for outer ROIs saved at 1
In an assignment A(:) = B, the number of elements in A and B must be the same.
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!
Linux jamestown.radiology.ucsf.edu 3.10.0-1062.1.2.el7.x86_64 #1 SMP Mon Sep 16
14:19:51 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s NDAR_INV021N0FLH exited with ERRORS at Tue Mar 3 11:09:41 PST 2020
For more details, see the log file
/working/ABCD/FS/NDAR_INV021N0FLH/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thank you for your time,
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
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