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Hello FreeSurfer Developers,
I am attempting to compute the local gfrification index(LGI), but is comes errors as below:
my command line is: recon-all -lgi -s AD02
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /opt/freesurfer
/usr/local/freesurfer/subjects/AD02/surf
#--------------------------------------------
#@# Local Gyrification Index lh Wed Aug 22 20:15:25 CST 2018
mris_compute_lgi --i lh.pial
=================
rm -Rf /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to /usr/local/freesurfer/subjects/AD02/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('/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/AD02/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 /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
=================
counting number of connected components...
64678 voxel in cpt #1: X=2 [v=64678,e=194028,f=129352] located at (-23.256193, -18.836494, 46.098969)
For the whole surface: X=2 [v=64678,e=194028,f=129352]
One single component has been found
nothing to do
done
=================
mris_smooth -nw -n 30 /usr/local/freesurfer/subjects/AD02/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: 64678 - 194028 + 129352 = 2 --> 0 holes
F =2V-4: 129352 = 129356-4 (0)
2E=3F: 388056 = 388056 (0)
total defect index = 0
=================
mris_convert -n lh.pial-outer-smoothed /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=================
=================
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_11463_.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 ( 0.03 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 =
6.5800
=================
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_11463_.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.
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 ( 0.03 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)
preparing outer mesh structure ...
face 5000 / 129352
face 10000 / 129352
face 15000 / 129352
face 20000 / 129352
face 25000 / 129352
face 30000 / 129352
face 35000 / 129352
face 40000 / 129352
face 45000 / 129352
face 50000 / 129352
face 55000 / 129352
face 60000 / 129352
face 65000 / 129352
face 70000 / 129352
face 75000 / 129352
face 80000 / 129352
face 85000 / 129352
face 90000 / 129352
face 95000 / 129352
face 100000 / 129352
face 105000 / 129352
face 110000 / 129352
face 115000 / 129352
face 120000 / 129352
face 125000 / 129352
mesh_outer =
vertices: [64678x3 double]
faces: [129352x3 double]
facesOfVertex: [64678x1 struct]
preparing pial mesh structure ...
...searching for mesh edges...done (165.42 sec).
... creating path file for vertex 1 / 64678
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 lishuyu 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s AD02 exited with ERRORS at Wed Aug 22 20:20:08 CST 2018
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I am looking forward for your reply!
best!
zhenrong fu
beihang university,beijing, china