Hello FS users,
I am using FreeSurfer version 5.3 to calculate local verification index and
processing stopped at make_roi_paths. Here, I was given the error below. I
searched in the archives and found a solution to the problem was to edit a few
lines on SearchProjectionOnPial.m. The new script is included below the error.
Any advice on how to fix this would be greatly appreciated.
Make_roi_paths error
=================
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/P0007/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_20907_.m');
exit
=================
< M A T L A B (R) >
Copyright 1984-2015 The MathWorks, Inc.
R2015b (8.6.0.267246) 64-bit (glnxa64)
August 20, 2015
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com<http://www.mathworks.com>.
modified_matlab =
/working/sdl_analysis/software/freesufer_5.3_matlab
Academic License
>> 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 ( 0.07 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 / 132292
face 10000 / 132292
face 15000 / 132292
face 20000 / 132292
face 25000 / 132292
face 30000 / 132292
face 35000 / 132292
face 40000 / 132292
face 45000 / 132292
face 50000 / 132292
face 55000 / 132292
face 60000 / 132292
face 65000 / 132292
face 70000 / 132292
face 75000 / 132292
face 80000 / 132292
face 85000 / 132292
face 90000 / 132292
face 95000 / 132292
face 100000 / 132292
face 105000 / 132292
face 110000 / 132292
face 115000 / 132292
face 120000 / 132292
face 125000 / 132292
face 130000 / 132292
mesh_outer =
vertices: [66148x3 double]
faces: [132292x3 double]
facesOfVertex: [66148x1 struct]
preparing pial mesh structure ...
...searching for mesh edges...done (140.10 sec).
... creating path file for vertex 1 / 66148
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);
SearchProjectionOnPial.m Script
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);
Sincerely,
Ryan Nillo
UCSF Center for Radiology and Biomedical Imaging
Staff Research Associate
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