Many thanks Doug for your reply!
For me it happened every time the lGI was launched, but none of the other
freesurfer commands that I used on this system ever resulted in a similar
error, everything else is perfectly fine. The process can hang for days without
going further, it will never come to the end.
For me the end of the recon-all.log read as reproduced below (with the load_mgh
in the file name). If I don't kill it, it will remain stuck at this point. The
matlab version may not be the issue, as Kangchen has a 2012 and my unix system
has a 2010 version. Freesurfer version is 5.3.
Thanks a lot for your help,
Marie
=================
make_outer_surface('/mnt/apricot1_share1/freesurfer_marie/UCLA_1_ABIDE/0051201/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/mnt/apricot1_share1/freesurfer_marie/UCLA_1_ABIDE/0051201/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 1984-2010 The MathWorks, Inc.
Version 7.11.0.584 (R2010b) 64-bit (glnxa64)
August 16, 2010
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com<http://www.mathworks.com/>.
reading filled volume...
copying file(s) to recycle bin..
removing file(s)..
/bin/rm: remove regular file `/tmp/tp9204736418620864.load_mgh.681685.mgh'?
On Dec 6, 2013, at 11:52 AM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
How often does it happen? Does the process just hang or does it produce
the correct results (eventually)? I don't think it is related to
load_mgh.m because the temporary filename would be different. However,
it is consistent with the temp files used with nifti reading and
writing. Does that happen in the lGI stream?
doug
On 12/06/2013 01:46 PM, Marie Schaer wrote:
Hi Kangchen,
I also had the same error recently on a unix machine, but I
unfortunately did not find the solution and some help would be greatly
appreciated.
I think that the bug is due to the fact that make_outer_surface.m
calls MRIread.m, which calls load_mgh.m and that something gets wrong
at the point of reading the file (and removing temporary files). But
I'm afraid I can't help more, I tried to edit load_mgh to add -f after
rm and it didn't help.
Nick or Doug, any idea?
Many thanks in advance!
Marie
On Dec 6, 2013, at 5:31 AM, 王康程
<kangchengwang0...@gmail.com<mailto:kangchengwang0...@gmail.com>
<mailto:kangchengwang0...@gmail.com>> wrote:
Dear all，
When I run "recon-all -s ${subject} -localGI", it appear "rm: remove
regular file `/tmp/tmp4653077.mgh'? ". Then, I write yes, however, it
didn't response anyway. How shold I do next? Thank you!
The echo for the process is followed
--------------------------
running subject Emotion_xunlian_s12002
--------------------------
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/fmri/desktop/test
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r--. 1 root root 544815 Dec 6 20:54
/home/fmri/desktop/test/Emotion_xunlian_s12002/scripts/recon-all.log
Linux localhost.localdomain 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct
16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf
#--------------------------------------------
#@# Local Gyrification Index lh Fri Dec 6 21:07:40 CST 2013
mris_compute_lgi --i lh.pial
=================
rm -Rf
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial
/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to
/home/fmri/desktop/test/Emotion_xunlian_s12002/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('/home/fmri/desktop/test/Emotion_xunlian_s12002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/home/fmri/desktop/test/Emotion_xunlian_s12002/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 1984-2012 The MathWorks, Inc.
R2012a (7.14.0.739) 64-bit (glnxa64)
February 9, 2012
Toolbox Path Cache read in 0.02 seconds.
MATLAB Path initialized in 0.79 seconds.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com<http://www.mathworks.com>
<http://www.mathworks.com/>.
reading filled volume...
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/fmri/desktop/test
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /opt/fsl
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/fmri/desktop/test
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /opt/fsl
rm: remove regular file `/tmp/tmp4653077.mgh'?
--
kangcheng Wang
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422
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_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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