error in local gyrification : error in dsearchn; error in mesh_vertex_nearest; reorganize_verticeslist.....
Dear freesurfer expert,
when I run 'recon-all -s subj -lgi' , I got the same error message for every subjects.
What does that mean? I really appreciate for your hint and help!
Here is the error message I got: ------------------------------------------------------------------------------------------------------------ spm@gonzo:/gdata1/freesurfer_data/subjects> recon-all -lgi -s AG01001 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /gdata1/freesurfer_data/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-rw- 1 spm users 724920 Feb 6 20:24 /gdata1/freesurfer_data/subjects/AG01001/scripts/recon-all.log Linux gonzo 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux /gdata1/freesurfer_data/subjects/AG01001/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Feb 7 14:23:51 CET 2014
mris_compute_lgi --i lh.pial
================= rm -Rf /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /gdata1/freesurfer_data/subjects/AG01001/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('/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main =================
counting number of connected components.. 67084 voxel in cpt #1: X=2 [v=67084,e=201246,f=134164] located at (-27.174467, -14.049744, 33.073147) For the whole surface: X=2 [v=67084,e=201246,f=134164] One single component has been found nothing to do done
================= mris_smooth -nw -n 30 /gdata1/freesurfer_data/subjects/AG01001/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: 67084 - 201246 + 134164 = 2 --> 0 holes F =2V-4: 134164 = 134168-4 (0) 2E=3F: 402492 = 402492 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_26868_.m'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.05 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 / 134164 face 10000 / 134164 face 15000 / 134164 face 20000 / 134164 face 25000 / 134164 face 30000 / 134164 face 35000 / 134164 face 40000 / 134164 face 45000 / 134164 face 50000 / 134164 face 55000 / 134164 face 60000 / 134164 face 65000 / 134164 face 70000 / 134164 face 75000 / 134164 face 80000 / 134164 face 85000 / 134164 face 90000 / 134164 face 95000 / 134164 .... mesh_outer =
vertices: [67084x3 double] faces: [134164x3 double] facesOfVertex: [67084x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (436.29 sec). ... creating path file for vertex 1 / 67084 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! Linux gonzo 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s AG01001 exited with ERRORS at Fri Feb 7 14:33:09 CET 2014
Thanks a lot for your help !
guoying
Hi Guoying,
Yes we have a bug with the more recent Matlab versions. You'll find all the details to solve it there:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30506.html
Let me know if it doesn't help,
Marie
On Feb 7, 2014, at 6:54 AM, "Wang, Guoying" <guoying.wang@zi-mannheim.demailto:guoying.wang@zi-mannheim.de> wrote:
Dear freesurfer expert,
when I run ‘recon-all –s subj –lgi‘ , I got the same error message for every subjects.
What does that mean? I really appreciate for your hint and help!
Here is the error message I got: ------------------------------------------------------------------------------------------------------------ spm@gonzo:/gdata1/freesurfer_data/subjects> recon-all -lgi -s AG01001 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /gdata1/freesurfer_data/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-rw- 1 spm users 724920 Feb 6 20:24 /gdata1/freesurfer_data/subjects/AG01001/scripts/recon-all.log Linux gonzo 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux /gdata1/freesurfer_data/subjects/AG01001/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Feb 7 14:23:51 CET 2014
mris_compute_lgi --i lh.pial
================= rm -Rf /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /gdata1/freesurfer_data/subjects/AG01001/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('/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.comhttp://www.mathworks.com.
reading filled volume...
closing volume... morphological closing done. writing outer surface...
================= mris_extract_main_component /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main =================
counting number of connected components.. 67084 voxel in cpt #1: X=2 [v=67084,e=201246,f=134164] located at (-27.174467, -14.049744, 33.073147) For the whole surface: X=2 [v=67084,e=201246,f=134164] One single component has been found nothing to do done
================= mris_smooth -nw -n 30 /gdata1/freesurfer_data/subjects/AG01001/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: 67084 - 201246 + 134164 = 2 --> 0 holes F =2V-4: 134164 = 134168-4 (0) 2E=3F: 402492 = 402492 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_26868_.m'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.comhttp://www.mathworks.com.
FREESURFER_READ_SURF [v 1.2 ]
...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.05 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 / 134164 face 10000 / 134164 face 15000 / 134164 face 20000 / 134164 face 25000 / 134164 face 30000 / 134164 face 35000 / 134164 face 40000 / 134164 face 45000 / 134164 face 50000 / 134164 face 55000 / 134164 face 60000 / 134164 face 65000 / 134164 face 70000 / 134164 face 75000 / 134164 face 80000 / 134164 face 85000 / 134164 face 90000 / 134164 face 95000 / 134164 .... mesh_outer =
vertices: [67084x3 double] faces: [134164x3 double] facesOfVertex: [67084x1 struct]
preparing pial mesh structure ... ...searching for mesh edges...done (436.29 sec). ... creating path file for vertex 1 / 67084 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! Linux gonzo 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s AG01001 exited with ERRORS at Fri Feb 7 14:33:09 CET 2014
Thanks a lot for your help !
guoying _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Marie Schaer -
Wang, Guoying