Hello experts,
I am using FreeSurfer version 6 and am trying to run recon-all -localGI. Each time I run it, it fails on make_roi_paths. Below is an excerpt of the recon-all.log file. Any help is much appreciated.
#@# Local Gyrification Index lh Thu Nov 9 14:06:42 PST 2017
mris_compute_lgi --i lh.pial
================= rm -Rf /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); 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.
Academic License
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main =================
counting number of connected components... 76848 voxel in cpt #1: X=2 [v=76848,e=230538,f=153692] located at (-26.925182, 5.953999, 4.185574) For the whole surface: X=2 [v=76848,e=230538,f=153692] One single component has been found nothing to do done
================= mris_smooth -nw -n 30 /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 76848 - 230538 + 153692 = 2 --> 0 holes F =2V-4: 153692 = 153696-4 (0) 2E=3F: 461076 = 461076 (0)
total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_8510_.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.
Academic License
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 ( 0.01 sec)
deltaT =
10.1400
================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_8510_.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.
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 / 153692 face 10000 / 153692 face 15000 / 153692 face 20000 / 153692 face 25000 / 153692 face 30000 / 153692 face 35000 / 153692 face 40000 / 153692 face 45000 / 153692 face 50000 / 153692 face 55000 / 153692 face 60000 / 153692 face 65000 / 153692 face 70000 / 153692 face 75000 / 153692 face 80000 / 153692 face 85000 / 153692 face 90000 / 153692 face 95000 / 153692 face 100000 / 153692 face 105000 / 153692 face 110000 / 153692 face 115000 / 153692 face 120000 / 153692 face 125000 / 153692 face 130000 / 153692 face 135000 / 153692 face 140000 / 153692 face 145000 / 153692 face 150000 / 153692
mesh_outer =
vertices: [76848x3 double] faces: [153692x3 double] facesOfVertex: [76848x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (189.57 sec). ... creating path file for vertex 1 / 76848 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 andaman.radiology.ucsf.edu 3.10.0-693.2.2.el7.x86_64 #1 SMP Sat Sep 9 03:55:24 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub_0015 exited with ERRORS at Thu Nov 9 14:11:33 PST 2017
For more details, see the log file /data/sugrue2/NF1_qdec/sub_0015/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thank you for your time,
Ryan Nillo