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.
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'?
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.commailto: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.comhttp://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
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'?
-- kangcheng Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.comhttp://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 <greve@nmr.mgh.harvard.edumailto:greve@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 <kangchengwang0808@gmail.commailto: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.comhttp://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, if yours had load_mgh in the file name, then it is definitely from load_mgh.m. Strange that the one below does not have that.
I think know what is going on. The rm command will sometimes ask if you want to remove a file, esp if you don't have write permissions. In general, if you create a file, you should have write perms, but there might be something strange that matlab is doing since it has to run a file externally to create the tmp file. Can you check that file to see what the perms are.
One fix may be to change each occurance of this line in load_mgh.m from if(gzipped >=0) unix(sprintf('rm %s', fname)); end to if(gzipped >=0) unix(sprintf('rm -f %s', fname)); end
There are about 5 places. Is this something that happens reliably so that you could test it?
doug
On 12/06/2013 03:02 PM, Marie Schaer wrote:
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, 2010To 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <kangchengwang0808@gmail.com mailto: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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I already tried changing all the occurrence of "rm" to "rm -f" in load_mgh.m, but it did not change anything. The error message remains identical.
The other strange thing is that, as the owner of the file, I have read and write permission on /tmp/tp9204736418620864.load_mgh.681685.mgh… Any other idea?
Thanks a lot for your help,
Marie
On Dec 6, 2013, at 1:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
OK, if yours had load_mgh in the file name, then it is definitely from load_mgh.m. Strange that the one below does not have that.
I think know what is going on. The rm command will sometimes ask if you want to remove a file, esp if you don't have write permissions. In general, if you create a file, you should have write perms, but there might be something strange that matlab is doing since it has to run a file externally to create the tmp file. Can you check that file to see what the perms are.
One fix may be to change each occurance of this line in load_mgh.m from if(gzipped >=0) unix(sprintf('rm %s', fname)); end to if(gzipped >=0) unix(sprintf('rm -f %s', fname)); end
There are about 5 places. Is this something that happens reliably so that you could test it?
doug
On 12/06/2013 03:02 PM, Marie Schaer wrote:
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, 2010To 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <kangchengwang0808@gmail.com mailto: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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is bizarre. The only other explanation is that the "you" who creates a file is not the same "you" who tries to delete it (it all sounds rather metaphysical:). Can you have that unix call run some unix commands to see who you are? Another thing is to make a unix command that creates a deletes a file. Is this something you can write a little matlab program to do or does it have to be run from inside recon-all?
doug
On 12/06/2013 04:24 PM, Marie Schaer wrote:
Hi Doug,
I already tried changing all the occurrence of "rm" to "rm -f" in load_mgh.m, but it did not change anything. The error message remains identical.
The other strange thing is that, as the owner of the file, I have read and write permission on /tmp/tp9204736418620864.load_mgh.681685.mgh… Any other idea?
Thanks a lot for your help,
Marie
On Dec 6, 2013, at 1:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
OK, if yours had load_mgh in the file name, then it is definitely from load_mgh.m. Strange that the one below does not have that.
I think know what is going on. The rm command will sometimes ask if you want to remove a file, esp if you don't have write permissions. In general, if you create a file, you should have write perms, but there might be something strange that matlab is doing since it has to run a file externally to create the tmp file. Can you check that file to see what the perms are.
One fix may be to change each occurance of this line in load_mgh.m from if(gzipped >=0) unix(sprintf('rm %s', fname)); end to if(gzipped >=0) unix(sprintf('rm -f %s', fname)); end
There are about 5 places. Is this something that happens reliably so that you could test it?
doug
On 12/06/2013 03:02 PM, Marie Schaer wrote:
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, 2010To 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <kangchengwang0808@gmail.com mailto: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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Marie Schaer, Thank you very much. I hope other experts could help me.
Kangcheng
Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
发件人： Marie Schaer 发送时间： 2013-12-07 02:46 收件人： 王康程 抄送： freesurfer@nmr.mgh.harvard.edu 主题： Re: [Freesurfer] LGI error
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 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.
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
kangchengwang0808＠gmail.com -
Marie Schaer -
王康程