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.comhttp://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