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:

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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) >

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) >

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