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 <kangchengwang0808@gmail.com mailto:kangchengwang0808@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/.
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'?
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