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 <gr...@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, 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
>>>>> _______________________________________________
>>>>> 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
>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@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
> gr...@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
