Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Anyway, after trying out the command with only one of the files from the tutorial,
*mri_concat --debug /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/y.mgh*
..the same thing happens, namely it returns to the command prompt, with no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
Tudor
On 20 December 2012 05:24, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
That does not make sense. Try using only one input file. Also, put --debug as the first option. doug
On 12/19/12 8:32 AM, Tudor Popescu wrote:
Hi Doug, So the full command is
mri_concat /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/141/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/084/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/021/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/093/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/080/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/091/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/040/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/017/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/138/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/106/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/108/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/092/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/124/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/129/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/103/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/130/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/039/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/123/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/095/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/067/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/004/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/133/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/097/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/073/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/149/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/045/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/136/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/144/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/032/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/131/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/145/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/111/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/102/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/074/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/114/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/008/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/128/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/099/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/lh-thickness-age-fwhm10/y.mgh --debug
..however, as soon as I press Enter, I'm just taken to the command prompt again, with no output whatsoever! Am I calling mri_concat wrongly?!
Tudor
On 18 December 2012 17:15, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Tudor, Can you run mri_concat from the command line with the --debug option first. Send us the FULL command line and the full terminal output. doug
On 12/18/2012 09:35 AM, Tudor Popescu wrote:
Hello everyone,
I tried doing the QDEC group analysis tutorial, however after doing everything as instructed in the tutorial, when pressing Analyze I get the error message:
/Error in Analyze: command failed: mri_concat
/media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh
(..)/
..even though those files are all accessible there! I pasted that same mri_concat manually into the terminal, however no output is produced at the command prompt, nor any files are created.
In previous attempts, I used to also get this error
/" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in SUBJECTS_DIR "/ /Syntax error: Bad fd number"/
after following the sh/bash workaround from this <
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.ht...
previous thread, I no longer get that error, however get stuck with the error mentioned above.
My SUBJECTS_DIR already contains a copy of the default subjects folder.
Debug info below. Any help greatly appreciated! Tudor
-------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/virtualuser/freesurfer FSFAST_HOME /home/virtualuser/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Dell/_FS/buckner_data/subjects MNI_DIR /home/virtualuser/freesurfer/mni
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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On 01/31/2013 12:30 PM, Tudor Popescu wrote:
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.
Anyway, after trying out the command with only one of the files from the tutorial,
/mri_concat --debug /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/y.mgh/
..the same thing happens, namely it returns to the command prompt, with no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
What happens if you type mri_concat with no options at all?
Tudor
On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That does not make sense. Try using only one input file. Also, put --debug as the first option. doug On 12/19/12 8:32 AM, Tudor Popescu wrote:Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/141/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/084/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/021/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/093/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/080/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/091/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/040/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/017/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/138/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/106/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/108/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/092/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/124/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/129/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/103/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/130/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/039/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/123/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/095/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/067/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/004/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/133/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/097/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/073/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/149/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/045/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/136/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/144/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/032/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/131/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/145/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/111/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/102/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/074/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/114/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/008/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/128/surf/lh.thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/subjects/099/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/lh-thickness-age-fwhm10/y.mgh --debug ..however, as soon as I press Enter, I'm just taken to the command prompt again, with no output whatsoever! Am I calling mri_concat wrongly?! Tudor On 18 December 2012 17:15, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Tudor, Can you run mri_concat from the command line with the --debug option first. Send us the FULL command line and the full terminal output. doug On 12/18/2012 09:35 AM, Tudor Popescu wrote: > Hello everyone, > > I tried doing the QDEC group analysis tutorial, however after doing > everything as instructed in the tutorial, when pressing Analyze I get > the error message: > > /Error in Analyze: command failed: mri_concat > /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh > (..)/ > > ..even though those files are all accessible there! I pasted that same > mri_concat manually into the terminal, however no output is produced > at the command prompt, nor any files are created. > > In previous attempts, I used to also get this error > > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in > SUBJECTS_DIR "/ > /Syntax error: Bad fd number"/ > > after following the sh/bash workaround from this > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.html>previous > thread, I no longer get that error, however get stuck with the error > mentioned above. > > My SUBJECTS_DIR already contains a copy of the default subjects folder. > > Debug info below. Any help greatly appreciated! > Tudor > > -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/virtualuser/freesurfer > FSFAST_HOME /home/virtualuser/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /media/Dell/_FS/buckner_data/subjects > MNI_DIR /home/virtualuser/freesurfer/mni > > > > _______________________________________________ > 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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <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 . 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Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
On 31 January 2013 20:36, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 01/31/2013 12:30 PM, Tudor Popescu wrote:
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.
Anyway, after trying out the command with only one of the files from the tutorial,
/mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/
..the same thing happens, namely it returns to the command prompt, with no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
What happens if you type mri_concat with no options at all?
Tudor
On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
That does not make sense. Try using only one input file. Also, put --debug as the first option. doug On 12/19/12 8:32 AM, Tudor Popescu wrote:Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** age-fwhm10/y.mgh --debug
..however, as soon as I press Enter, I'm just taken to the command prompt again, with no output whatsoever! Am I calling mri_concat wrongly?! Tudor On 18 December 2012 17:15, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote:
Hi Tudor, Can you run mri_concat from the command line with the --debug option first. Send us the FULL command line and the full terminal output. doug On 12/18/2012 09:35 AM, Tudor Popescu wrote: > Hello everyone, > > I tried doing the QDEC group analysis tutorial, however after doing > everything as instructed in the tutorial, when pressing Analyze I get > the error message: > > /Error in Analyze: command failed: mri_concat > /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh > /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** thickness.fwhm10.fsaverage.mgh > (..)/ > > ..even though those files are all accessible there! I pasted that same > mri_concat manually into the terminal, however no output is produced > at the command prompt, nor any files are created. > > In previous attempts, I used to also get this error > > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in > SUBJECTS_DIR "/ > /Syntax error: Bad fd number"/ > > after following the sh/bash workaround from this > <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-** October/008618.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.html
previous
> thread, I no longer get that error, however get stuck with the error > mentioned above. > > My SUBJECTS_DIR already contains a copy of the default subjects folder. > > Debug info below. Any help greatly appreciated! > Tudor > > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/virtualuser/freesurfer > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > MNI_DIR /home/virtualuser/freesurfer/**mni > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote:
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
On 31 January 2013 20:36, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 01/31/2013 12:30 PM, Tudor Popescu wrote:
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.
Anyway, after trying out the command with only one of the files from the tutorial,
/mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/
..the same thing happens, namely it returns to the command prompt, with no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
What happens if you type mri_concat with no options at all?
Tudor
On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote: That does not make sense. Try using only one input file. Also, put --debug as the first option. doug
On 12/19/12 8:32 AM, Tudor Popescu wrote:Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/049/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/141/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/084/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/021/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/093/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/080/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/091/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/040/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/017/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/138/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/106/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/108/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/092/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/124/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/129/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/103/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/130/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/039/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/123/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/095/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/067/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/004/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/133/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/097/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/073/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/149/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/045/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/136/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/144/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/032/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/131/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/145/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/111/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/102/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/074/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/114/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/008/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/128/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/099/surf/lh.**thickness.fwhm10.fsaverage.mgh
--o /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-**age-fwhm10/y.mgh
--debug ..however, as soon as I press Enter, I'm just taken to the command prompt again, with no output whatsoever! Am I calling mri_concat wrongly?! Tudor On 18 December 2012 17:15, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote: Hi Tudor, Can you run mri_concat from the command line with the --debug option first. Send us the FULL command line and the full terminal output. doug
On 12/18/2012 09:35 AM, Tudor Popescu wrote: > Hello everyone, > > I tried doing the QDEC group analysis tutorial, however after doing > everything as instructed in the tutorial, when pressing Analyze I get > the error message: > > /Error in Analyze: command failed: mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/049/surf/lh.**thickness.fwhm10.fsaverage.mgh
> (..)/ > > ..even though those files are all accessible there! I pasted that same > mri_concat manually into the terminal, however no output is produced > at the command prompt, nor any files are created. > > In previous attempts, I used to also get this error > > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in > SUBJECTS_DIR "/ > /Syntax error: Bad fd number"/ > > after following the sh/bash workaround from this <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-* *October/008618.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurf er/2008-October/008618.html
previous
> thread, I no longer get that error, however get stuck with the error > mentioned above. > > My SUBJECTS_DIR already contains a copy of the default subjects folder. > Debug info below. Any help greatly appreciated! > Tudor > > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 > -------- Setting up environment for FreeSurfer/FS-FAST (and > FSL) FREESURFER_HOME /home/virtualuser/freesurfer > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > MNI_DIR /home/virtualuser/freesurfer/**mni > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.har vard.edu> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer .nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<htt p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://w ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.har vard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe r<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<http://www.partners.or g/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.-- 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/BugReportinghttp://surfer.nmr.mgh.h arvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mg h.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi surfers,
sorry to bump this, but i seem to have the exact same problem:
- qdec informs me that mri_concat failed - mri_concat itself produces no output at all - also not with --debug or without any arguments at all - however, mri_concat has a non-zero exit status
btw, i also ran into the sh syntax error, which i worked around by linking sh to bash. i assume this is not directly related, but maybe Tudor and i share the same platform, to which both problems are related?
i am using the 32bit centOS4 build on debian 7.
greetings from Vienna Andreas
Hi Andreas
I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL..
Tudor
On 18 March 2013 11:13, Andreas Berger n0642496@students.meduniwien.ac.atwrote:
On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote:
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after
the
file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
On 31 January 2013 20:36, Douglas N Greve greve@nmr.mgh.harvard.edu
wrote:
On 01/31/2013 12:30 PM, Tudor Popescu wrote:
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.
Anyway, after trying out the command with only one of the files from
the
tutorial,
/mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/
..the same thing happens, namely it returns to the command prompt,
with
no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
What happens if you type mri_concat with no options at all?
Tudor
On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote: That does not make sense. Try using only one input file. Also, put --debug as the first option. doug
On 12/19/12 8:32 AM, Tudor Popescu wrote:Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/049/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/141/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/084/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/021/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/093/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/080/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/091/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/040/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/017/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/138/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/106/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/108/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/092/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/124/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/129/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/103/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/130/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/039/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/123/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/095/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/067/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/004/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/133/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/097/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/073/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/149/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/045/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/136/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/144/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/032/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/131/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/145/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/111/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/102/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/074/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/114/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/008/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/128/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/099/surf/lh.**thickness.fwhm10.fsaverage.mgh
--o /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-**age-fwhm10/y.mgh
--debug ..however, as soon as I press Enter, I'm just taken to the command prompt again, with no output whatsoever! Am I calling mri_concat wrongly?! Tudor On 18 December 2012 17:15, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote: Hi Tudor, Can you run mri_concat from the command line with the --debug option first. Send us the FULL command line and the full terminal output. doug
On 12/18/2012 09:35 AM, Tudor Popescu wrote: > Hello everyone, > > I tried doing the QDEC group analysis tutorial, however after doing > everything as instructed in the tutorial, when pressing Analyze I get > the error message: > > /Error in Analyze: command failed: mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/049/surf/lh.**thickness.fwhm10.fsaverage.mgh
> (..)/ > > ..even though those files are all accessible there! I pasted that same > mri_concat manually into the terminal, however no output is produced > at the command prompt, nor any files are created. > > In previous attempts, I used to also get this error > > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in > SUBJECTS_DIR "/ > /Syntax error: Bad fd number"/ > > after following the sh/bash workaround from this <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-*
*October/008618.html<
https://mail.nmr.mgh.harvard.edu/pipermail/freesurf
er/2008-October/008618.html>
previous
> thread, I no longer get that error, however get stuck with the error > mentioned above. > > My SUBJECTS_DIR already contains a copy of the default subjects folder. > Debug info below. Any help greatly appreciated! > Tudor > > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 > -------- Setting up environment for FreeSurfer/FS-FAST (and > FSL) FREESURFER_HOME /home/virtualuser/freesurfer > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > MNI_DIR /home/virtualuser/freesurfer/**mni > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.har
vard.edu> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<
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<greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<htt
p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://w
ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht
ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ <
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.har
vard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe
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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<g/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.-- 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<
arvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<
h.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi surfers,
sorry to bump this, but i seem to have the exact same problem:
- qdec informs me that mri_concat failed
- mri_concat itself produces no output at all
- also not with --debug or without any arguments at all
- however, mri_concat has a non-zero exit status
btw, i also ran into the sh syntax error, which i worked around by linking sh to bash. i assume this is not directly related, but maybe Tudor and i share the same platform, to which both problems are related?
i am using the 32bit centOS4 build on debian 7.
greetings from Vienna Andreas
Just giving this thread a new bump, as *again *I am receiving this error from mri_concat, upon pressing the Analyze button in QDEC. Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and includes a copy of the fsaverage folder) and all files included in the error are at the expected path. Screenshot attached.
On 18 March 2013 11:20, Tudor Popescu tudor3@gmail.com wrote:
Hi Andreas
I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL..
Tudor
On 18 March 2013 11:13, Andreas Berger <n0642496@students.meduniwien.ac.at
wrote:
On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote:
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after
the
file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked.
Also,
the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been
working
all this time, especially since I didn't really do anything different
now
(that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
On 31 January 2013 20:36, Douglas N Greve greve@nmr.mgh.harvard.edu
wrote:
On 01/31/2013 12:30 PM, Tudor Popescu wrote:
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.
Anyway, after trying out the command with only one of the files from
the
tutorial,
/mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/
..the same thing happens, namely it returns to the command prompt,
with
no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
What happens if you type mri_concat with no options at all?
Tudor
On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote: That does not make sense. Try using only one input file. Also,
put
--debug as the first option. doug On 12/19/12 8:32 AM, Tudor Popescu wrote:Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/049/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/141/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/084/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/021/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/093/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/080/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/091/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/040/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/017/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/138/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/106/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/108/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/092/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/124/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/129/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/103/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/130/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/039/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/123/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/095/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/067/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/004/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/133/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/097/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/073/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/149/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/045/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/136/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/144/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/032/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/131/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/145/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/111/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/102/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/074/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/114/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/008/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/128/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/099/surf/lh.**thickness.fwhm10.fsaverage.mgh
--o /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-**age-fwhm10/y.mgh
--debug ..however, as soon as I press Enter, I'm just taken to the command prompt again, with no output whatsoever! Am I calling mri_concat wrongly?! Tudor On 18 December 2012 17:15, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.eduwrote: Hi Tudor, Can you run mri_concat from the command line with the
--debug
option first. Send us the FULL command line and the full terminal output. doug On 12/18/2012 09:35 AM, Tudor Popescu wrote: > Hello everyone, > > I tried doing the QDEC group analysis tutorial, however after doing > everything as instructed in the tutorial, when pressing Analyze I get > the error message: > > /Error in Analyze: command failed: mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.**thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/**subjects/049/surf/lh.**thickness.fwhm10.fsaverage.mgh
> (..)/ > > ..even though those files are all accessible there! I pasted that same > mri_concat manually into the terminal, however no outputis
produced > at the command prompt, nor any files are created. > > In previous attempts, I used to also get this error > > /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in > SUBJECTS_DIR "/ > /Syntax error: Bad fd number"/ > > after following the sh/bash workaround from this <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-*
*October/008618.html<
https://mail.nmr.mgh.harvard.edu/pipermail/freesurf
er/2008-October/008618.html>
>previous > > thread, I no longer get that error, however get stuck with
the error > mentioned above. > > My SUBJECTS_DIR already contains a copy of the default subjects folder. > Debug info below. Any help greatly appreciated! > Tudor > > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 > -------- Setting up environment for FreeSurfer/FS-FAST(and
> FSL) FREESURFER_HOME /home/virtualuser/freesurfer > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > MNI_DIR /home/virtualuser/freesurfer/**mni > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.har
vard.edu> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<
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<greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<htt
p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://w
ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht
ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/ <
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.har
vard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe
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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<g/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.-- 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<
arvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<
h.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi surfers,
sorry to bump this, but i seem to have the exact same problem:
- qdec informs me that mri_concat failed
- mri_concat itself produces no output at all
- also not with --debug or without any arguments at all
- however, mri_concat has a non-zero exit status
btw, i also ran into the sh syntax error, which i worked around by linking sh to bash. i assume this is not directly related, but maybe Tudor and i share the same platform, to which both problems are related?
i am using the 32bit centOS4 build on debian 7.
greetings from Vienna Andreas
Still stuck with this error in my QDEC analysis attempt, at my wit's end, could anyone help please? Thanks! Tudor
On 26 March 2013 20:35, Tudor Popescu tudor3@gmail.com wrote:
Just giving this thread a new bump, as *again *I am receiving this error from mri_concat, upon pressing the Analyze button in QDEC. Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and includes a copy of the fsaverage folder) and all files included in the error are at the expected path. Screenshot attached.
On 18 March 2013 11:20, Tudor Popescu tudor3@gmail.com wrote:
Hi Andreas
I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL..
Tudor
On 18 March 2013 11:13, Andreas Berger < n0642496@students.meduniwien.ac.at> wrote:
On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote:
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just
after the
file name, which should not have been there; although having tried
again
with the backslash reinstated at the end, the command still worked.
Also,
the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been
working
all this time, especially since I didn't really do anything different
now
(that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
On 31 January 2013 20:36, Douglas N Greve greve@nmr.mgh.harvard.edu
wrote:
On 01/31/2013 12:30 PM, Tudor Popescu wrote:
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong,
rather
that the behavior did not make sense -- it should print *something*
to
the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.
Anyway, after trying out the command with only one of the files
from the
tutorial,
/mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/
..the same thing happens, namely it returns to the command prompt,
with
no message whatsoever.
What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!
What happens if you type mri_concat with no options at all?
Tudor
On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote: That does not make sense. Try using only one input file. Also,
put
--debug as the first option. doug On 12/19/12 8:32 AM, Tudor Popescu wrote:> Hi Doug, > So the full command is > > mri_concat > /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > --o > /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > > age-fwhm10/y.mgh > > --debug > > ..however, as soon as I press Enter, I'm just taken to the > command prompt again, with no output whatsoever! Am I calling > mri_concat wrongly?! > > Tudor > > On 18 December 2012 17:15, Douglas N Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu
> > wrote: > Hi Tudor, > Can you run mri_concat from the command line with the
--debug
> option > first. Send us the FULL command line and the full terminal > output. > doug > > On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > Hello everyone, > > > > I tried doing the QDEC group analysis tutorial, however > > after doing > > > everything as instructed in the tutorial, when pressing > > Analyze I get > > > the error message: > > > > /Error in Analyze: command failed: mri_concat > > /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > thickness.fwhm10.fsaverage.mgh > > > (..)/ > > > > ..even though those files are all accessible there! I > > pasted that same > > > mri_concat manually into the terminal, however no output
is
> > produced > > > at the command prompt, nor any files are created. > > > > In previous attempts, I used to also get this error > > > > /" .ERROR: QdecProject::VerifySubjects: Couldn't find > > subject '032' in > > > SUBJECTS_DIR "/ > > /Syntax error: Bad fd number"/ > > > > after following the sh/bash workaround from this > > <https://mail.nmr.mgh.harvard.
**edu/pipermail/freesurfer/2008-*
> * > > October/008618.html<
https://mail.nmr.mgh.harvard.edu/pipermail/freesurf
> er/2008-October/008618.html> > > >previous > > > > thread, I no longer get that error, however get stuck
with
> > the error > > > mentioned above. > > > > My SUBJECTS_DIR already contains a copy of the default > > subjects folder. > > > Debug info below. Any help greatly appreciated! > > Tudor > > > > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 > > -------- Setting up environment for FreeSurfer/FS-FAST
(and
> > FSL) FREESURFER_HOME /home/virtualuser/freesurfer > > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > > MNI_DIR /home/virtualuser/freesurfer/**mni > > > > > > > > ______________________________**_________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.**harvard.edu
<Freesurfer@nmr.mgh.har
> vard.edu> > > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > > freesurfer<
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<
greve@nmr.mgh.harvard.edu>
> > > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<
> .nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting
<htt
> p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<
http://w
> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.
**edu/facility/filedrop/index.**ht
> ml<
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.
**edu/transfer/outgoing/flat/**
> > greve/ <
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.**harvard.edu
<Freesurfer@nmr.mgh.har
> vard.edu> > > > https://mail.nmr.mgh.harvard.
**edu/mailman/listinfo/**freesurfe
> r<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
> > > 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<
> g/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.
-- 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<
arvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<
h.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi surfers,
sorry to bump this, but i seem to have the exact same problem:
- qdec informs me that mri_concat failed
- mri_concat itself produces no output at all
- also not with --debug or without any arguments at all
- however, mri_concat has a non-zero exit status
btw, i also ran into the sh syntax error, which i worked around by linking sh to bash. i assume this is not directly related, but maybe Tudor and i share the same platform, to which both problems are related?
i am using the 32bit centOS4 build on debian 7.
greetings from Vienna Andreas
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC?
On 03/28/2013 03:51 PM, Tudor Popescu wrote:
Still stuck with this error in my QDEC analysis attempt, at my wit's end, could anyone help please? Thanks! Tudor
On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
Just giving this thread a new bump, as /again /I am receiving this error from mri_concat, upon pressing the Analyze button in QDEC. Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and includes a copy of the fsaverage folder) and all files included in the error are at the expected path. Screenshot attached. On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com>> wrote: Hi Andreas I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL.. Tudor On 18 March 2013 11:13, Andreas Berger <n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>> wrote: On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > Hi Doug > > Strangely, the basic mri_concat command now worked, and so did the full > one. I think I initially had a "\" at the end of my command, just after the > file name, which should not have been there; although having tried again > with the backslash reinstated at the end, the command still worked. Also, > the Analyze in the QDEC GUI now completes without error as well. > > It's quite frustrating that I still don't know why it hasn't been working > all this time, especially since I didn't really do anything different now > (that I was aware of!) and the files were located on the same partition > (Virtualbox's shared folder). > > Anyhow, thanks again for your kind help! > > Tudor > > On 31 January 2013 20:36, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > >> Hi Doug, > >> > >> I'm not sure why that does not make sense, shouldn't the input of > >> mri_concat be several to-be-concatenated files rather than a single > >> file? > > > > Sorry, I did not mean to imply that the command line was wrong, rather > > that the behavior did not make sense -- it should print *something* to > > the terminal. It does make sense to have multiple files, but it will > > also work with a single file. I just suggested this to make things > > simpler. > > > >> Anyway, after trying out the command with only one of the files from the > >> tutorial, > >> > >> /mri_concat --debug > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > >> *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** > >> subjects/qdec/y.mgh/ > >> > >> > >> ..the same thing happens, namely it returns to the command prompt, with > >> no message whatsoever. > >> > >> What could be wrong? As I mentioned, all those MGH files are at the > >> expected path. Thanks again for your help! > > > > What happens if you type mri_concat with no options at all? > > > >> Tudor > >> > >> > >> On 20 December 2012 05:24, Douglas Greve > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto: > >> > >> greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > >> That does not make sense. Try using only one input file. Also, put > >> --debug as the first option. > >> doug > >> > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > >>> Hi Doug, > >>> So the full command is > >>> > >>> mri_concat > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> --o > >>> /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > >>> > >>> age-fwhm10/y.mgh > >>> > >>> --debug > >>> > >>> ..however, as soon as I press Enter, I'm just taken to the > >>> command prompt again, with no output whatsoever! Am I calling > >>> mri_concat wrongly?! > >>> > >>> Tudor > >>> > >>> On 18 December 2012 17:15, Douglas N Greve > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >>> <mailto:greve@nmr.mgh.harvard. <mailto:greve@nmr.mgh.harvard.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > >>> > >>> wrote: > >>> Hi Tudor, > >>> Can you run mri_concat from the command line with the --debug > >>> option > >>> first. Send us the FULL command line and the full terminal > >>> output. > >>> doug > >>> > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > >>> > Hello everyone, > >>> > > >>> > I tried doing the QDEC group analysis tutorial, however > >>> > >>> after doing > >>> > >>> > everything as instructed in the tutorial, when pressing > >>> > >>> Analyze I get > >>> > >>> > the error message: > >>> > > >>> > /Error in Analyze: command failed: mri_concat > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> > (..)/ > >>> > > >>> > ..even though those files are all accessible there! I > >>> > >>> pasted that same > >>> > >>> > mri_concat manually into the terminal, however no output is > >>> > >>> produced > >>> > >>> > at the command prompt, nor any files are created. > >>> > > >>> > In previous attempts, I used to also get this error > >>> > > >>> > /" .ERROR: QdecProject::VerifySubjects: Couldn't find > >>> > >>> subject '032' in > >>> > >>> > SUBJECTS_DIR "/ > >>> > /Syntax error: Bad fd number"/ > >>> > > >>> > after following the sh/bash workaround from this > >>> > >>> <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-* > >>> * > >>> > >>> October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf > >>> er/2008-October/008618.html> > >>> > >>> >previous > >>> > > >>> > thread, I no longer get that error, however get stuck with > >>> > >>> the error > >>> > >>> > mentioned above. > >>> > > >>> > My SUBJECTS_DIR already contains a copy of the default > >>> > >>> subjects folder. > >>> > >>> > Debug info below. Any help greatly appreciated! > >>> > Tudor > >>> > > >>> > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 > >>> > -------- Setting up environment for FreeSurfer/FS-FAST (and > >>> > FSL) FREESURFER_HOME /home/virtualuser/freesurfer > >>> > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > >>> > FSF_OUTPUT_FORMAT nii.gz > >>> > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > >>> > > >>> > > >>> > > >>> > ______________________________**_________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> > >>> <mailto:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>**harvard.edu <http://harvard.edu><Freesurfer@nmr.mgh.har > >>> vard.edu <http://vard.edu>> > >>> > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > >>> > >>> freesurfer<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> > >>> <mailto:greve@nmr.mgh.harvard. <mailto:greve@nmr.mgh.harvard.>**edu<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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting><htt > >>> p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > >>> > >>> FileDrop: > >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://w > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht > >>> ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > >>> > >>> Outgoing: > >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > >>> > >>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >>> > >>> ______________________________**_________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> <mailto:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>**harvard.edu <http://harvard.edu><Freesurfer@nmr.mgh.har > >>> vard.edu <http://vard.edu>> > >>> > >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe > >>> r<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<http://www.partners.or > >>> g/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. > > > > -- > > 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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.h > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://www.nmr.mg > > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html>> Outgoing: > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> Hi surfers, sorry to bump this, but i seem to have the exact same problem: - qdec informs me that mri_concat failed - mri_concat itself produces no output at all - also not with --debug or without any arguments at all - however, mri_concat has a non-zero exit status btw, i also ran into the sh syntax error, which i worked around by linking sh to bash. i assume this is not directly related, but maybe Tudor and i share the same platform, to which both problems are related? i am using the 32bit centOS4 build on debian 7. greetings from Vienna Andreas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt.
The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz
Could this indicate something is wrong with the mri_concat command itself?
On 28 March 2013 20:01, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC?
On 03/28/2013 03:51 PM, Tudor Popescu wrote:
Still stuck with this error in my QDEC analysis attempt, at my wit's end, could anyone help please? Thanks! Tudor
On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
Just giving this thread a new bump, as /again /I am receiving this error from mri_concat, upon pressing the Analyze button in QDEC. Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and includes a copy of the fsaverage folder) and all files included in the error are at the expected path. Screenshot attached. On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com>> wrote: Hi Andreas I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL.. Tudor On 18 March 2013 11:13, Andreas Berger <n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>> wrote: On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > Hi Doug > > Strangely, the basic mri_concat command now worked, and so did the full > one. I think I initially had a "\" at the end of my command, just after the > file name, which should not have been there; although having tried again > with the backslash reinstated at the end, the command still worked. Also, > the Analyze in the QDEC GUI now completes without error as well. > > It's quite frustrating that I still don't know why it hasn't been working > all this time, especially since I didn't really do anything different now > (that I was aware of!) and the files were located on the same partition > (Virtualbox's shared folder). > > Anyhow, thanks again for your kind help! > > Tudor > > On 31 January 2013 20:36, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > >> Hi Doug, > >> > >> I'm not sure why that does not make sense, shouldn't the input of > >> mri_concat be several to-be-concatenated files rather than a single > >> file? > > > > Sorry, I did not mean to imply that the command line was wrong, rather > > that the behavior did not make sense -- it should print *something* to > > the terminal. It does make sense to have multiple files, but it will > > also work with a single file. I just suggested this to make things > > simpler. > > > >> Anyway, after trying out the command with only one of the files from the > >> tutorial, > >> > >> /mri_concat --debug > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > >> *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** > >> subjects/qdec/y.mgh/ > >> > >> > >> ..the same thing happens, namely it returns to the command prompt, with > >> no message whatsoever. > >> > >> What could be wrong? As I mentioned, all those MGH files are at the > >> expected path. Thanks again for your help! > > > > What happens if you type mri_concat with no options at all? > > > >> Tudor > >> > >> > >> On 20 December 2012 05:24, Douglas Greve > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto: > >> > >> greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > >> That does not make sense. Try using only one input file. Also, put > >> --debug as the first option. > >> doug > >> > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > >>> Hi Doug, > >>> So the full command is > >>> > >>> mri_concat > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> --o > >>> /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > >>> > >>> age-fwhm10/y.mgh > >>> > >>> --debug > >>> > >>> ..however, as soon as I press Enter, I'm just taken to the > >>> command prompt again, with no output whatsoever! Am I calling > >>> mri_concat wrongly?! > >>> > >>> Tudor > >>> > >>> On 18 December 2012 17:15, Douglas N Greve > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >>> <mailto:greve@nmr.mgh.harvard. <mailto:greve@nmr.mgh.harvard.>**edu<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> > >>> > >>> wrote: > >>> Hi Tudor, > >>> Can you run mri_concat from the command line with the --debug > >>> option > >>> first. Send us the FULL command line and the full terminal > >>> output. > >>> doug > >>> > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > >>> > Hello everyone, > >>> > > >>> > I tried doing the QDEC group analysis tutorial, however > >>> > >>> after doing > >>> > >>> > everything as instructed in the tutorial, when pressing > >>> > >>> Analyze I get > >>> > >>> > the error message: > >>> > > >>> > /Error in Analyze: command failed: mri_concat > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > >>> > >>> thickness.fwhm10.fsaverage.mgh > >>> > >>> > (..)/ > >>> > > >>> > ..even though those files are all accessible there! I > >>> > >>> pasted that same > >>> > >>> > mri_concat manually into the terminal, however no output is > >>> > >>> produced > >>> > >>> > at the command prompt, nor any files are created. > >>> > > >>> > In previous attempts, I used to also get this error > >>> > > >>> > /" .ERROR: QdecProject::VerifySubjects: Couldn't find > >>> > >>> subject '032' in > >>> > >>> > SUBJECTS_DIR "/ > >>> > /Syntax error: Bad fd number"/ > >>> > > >>> > after following the sh/bash workaround from this > >>> > >>> <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-*
> >>> * > >>> > >>> October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf
> >>> er/2008-October/008618.html> > >>> > >>> >previous > >>> > > >>> > thread, I no longer get that error, however get stuck with > >>> > >>> the error > >>> > >>> > mentioned above. > >>> > > >>> > My SUBJECTS_DIR already contains a copy of the default > >>> > >>> subjects folder. > >>> > >>> > Debug info below. Any help greatly appreciated! > >>> > Tudor > >>> > > >>> > -------- freesurfer-Linux-centos4-**stable-pub-v5.1.0 > >>> > -------- Setting up environment for FreeSurfer/FS-FAST (and > >>> > FSL) FREESURFER_HOME /home/virtualuser/freesurfer > >>> > FSFAST_HOME /home/virtualuser/freesurfer/**fsfast > >>> > FSF_OUTPUT_FORMAT nii.gz > >>> > SUBJECTS_DIR /media/Dell/_FS/buckner_data/**subjects > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > >>> > > >>> > > >>> > > >>> > ______________________________**_________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> > >>> <mailto:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>**harvard.edu <http://harvard.edu><Freesurfer@nmr.mgh.har > >>> vard.edu <http://vard.edu>> > >>> > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > >>> > >>> freesurfer<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> > >>> <mailto:greve@nmr.mgh.harvard. <mailto:greve@nmr.mgh.harvard.>**edu<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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><> >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting><htt > >>> p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > >>> > >>> FileDrop: > >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E<http://w
> >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht
> >>> ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
> >>> > >>> > >>> Outgoing: > >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > >>> > >>> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >>> > >>> ______________________________**_________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> <mailto:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>**harvard.edu <http://harvard.edu><Freesurfer@nmr.mgh.har > >>> vard.edu <http://vard.edu>> > >>> > >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe
> >>> r<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
> >>> > >>> > >>> 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<> >>> g/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. > > > > -- > > 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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><> > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E< http://www.nmr.mg
> > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html>>Outgoing:
> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
Hi surfers, sorry to bump this, but i seem to have the exact sameproblem:
- qdec informs me that mri_concat failed - mri_concat itself produces no output at all - also not with --debug or without any arguments at all - however, mri_concat has a non-zero exit status btw, i also ran into the sh syntax error, which i worked around by linking sh to bash. i assume this is not directly related, but maybe Tudor and i share the same platform, to which both problems are related? i am using the 32bit centOS4 build on debian 7. greetings from Vienna Andreas
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-- 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: 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
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.
If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on?
On 03/28/2013 04:17 PM, Tudor Popescu wrote:
I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt.
The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz
Could this indicate something is wrong with the mri_concat command itself?
On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> > <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>>> wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "\" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.mgh --o > /media/Dell/_FS/buckner_data/** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>><mailto: > > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as I press Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> > > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze: command failed: mri_concat > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though those files are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-**stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/**fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/**subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________**_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>.>**harvard.edu <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer > > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting> > <http://harvard.edu/fswiki/**BugReporting><htt > > >>> > p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://w > > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > >>> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht > > >>> > ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > >>> > > >>> ______________________________**_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>.>**harvard.edu <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe > > >>> > r<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<http://www.partners.or > > >>> g/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. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.h > > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting> > <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://www.nmr.mg > > > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html> > <http://h.harvard.edu/facility/filedrop/index.html>> Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna > Andreas > > > > > > > _______________________________________________ > 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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <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.
I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is 1.4 THanks for your help
On 29 March 2013 17:33, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on?
On 03/28/2013 04:17 PM, Tudor Popescu wrote:
I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt.
The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz
Could this indicate something is wrong with the mri_concat command itself?
On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.**ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>>>>wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.**mgh --o > /media/Dell/_FS/buckner_data/**** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:
> > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>>wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/****subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as I press Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > > >>> <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**.>**edu<greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>> > > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze: command failed: mri_concat > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though those files are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.****edu/pipermail/freesurfer/**2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://** mail.nmr.mgh.harvard.edu/**pipermail/freesurfhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-****stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/****fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/****subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/****mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________****_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > >>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>.>****harvard.edu <http://harvard.edu> > <http://harvard.edu><**Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<https://mail.nmr.**mgh.harvard.edu/mailman/**listinfo/freesurferhttps://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 greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > > >>> <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**.>**edu<greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>> > > >>> > > >>> > > >>> Phone Number: 617-724-2358 > > >>> Fax: 617-726-7422 > > >>> > > >>> Bugs: > > >>> surfer.nmr.mgh.harvard.edu/****fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>< http://surfer > > >>> .nmr.mgh.harvard.edu/fswiki/** BugReporting http://nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://nmr.mgh.harvard.edu/**fswiki/BugReporting<http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > >>> > <http://surfer.nmr.mgh.**harva**rd.edu/fswiki/**BugReporting http://harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/****BugReportinghttp://harvard.edu/fswiki/**BugReporting
> <http://harvard.edu/fswiki/****BugReporting<http://harvard.edu/fswiki/**BugReporting><htt
> > >>> > p://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/****facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
<http://w
> > >>> ww.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://ww.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>> > <http://www.nmr.mgh.harvard.****edu/facility/filedrop/index.****ht > > >>> > ml<http://www.nmr.mgh.harvard.** edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.****edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >>> > > >>> ______________________________****_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>.>****harvard.edu <http://harvard.edu> > <http://harvard.edu><**Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/****freesurfe > > >>> > r<https://mail.nmr.mgh.**harvard.edu/mailman/listinfo/**freesurferhttps://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<http://www.partners.org/**complianceline><http://www.**partners.or http://www.partners.or > > >>> g/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. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: > > > surfer.nmr.mgh.harvard.edu/****fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>< http://surfer.**nmr.mgh.h http://surfer.nmr.mgh.h > > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/**BugReportinghttp://arvard.edu/fswiki/BugReporting
> <http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting>>>FileDrop: > > > www.nmr.mgh.harvard.edu/****facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> > > h.harvard.edu/facility/**filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/**facility/filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html>> <http://h.harvard.edu/**facility/filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html>Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.****edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna > Andreas > > > > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Do you know if that version works outside of Virtualbox?
On 03/29/2013 03:13 PM, Tudor Popescu wrote:
I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is 1.4 THanks for your help
On 29 March 2013 17:33, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on? On 03/28/2013 04:17 PM, Tudor Popescu wrote: I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt. The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz Could this indicate something is wrong with the mri_concat command itself? On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>> wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>> > <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>>>> wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "\" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.mgh --o > /media/Dell/_FS/buckner_data/** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>><mailto: > > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as I press Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>> > > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze: command failed: mri_concat > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though those files are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-**stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/**fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/**subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________**_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>.>**harvard.edu <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer > > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> > <http://harvard.edu/fswiki/**BugReporting><htt > > >>> > p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://w > > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > >>> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht > > >>> > ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > >>> > > >>> ______________________________**_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>.>**harvard.edu <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe > > >>> > r<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<http://www.partners.or > > >>> g/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. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.h > > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> > <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://www.nmr.mg > > > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> > <http://h.harvard.edu/facility/filedrop/index.html>> Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna > Andreas > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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 <mailto: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. -- 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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Not sure what you mean .. Since I'm on Windows, without access to a Linux machine, I have to run it through Virtualbox.
It's strange how all other FS commands seem to work, but mri_concat is the only one that returns me straight to the command line. Could it have somehow become corrupt (although I can't think why that would have happened)?
On 29 March 2013 19:17, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Do you know if that version works outside of Virtualbox?
On 03/29/2013 03:13 PM, Tudor Popescu wrote:
I'm running freesurfer-Linux-centos4-**stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is 1.4 THanks for your help
On 29 March 2013 17:33, Douglas N Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on? On 03/28/2013 04:17 PM, Tudor Popescu wrote: I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt. The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz Could this indicate something is wrong with the mri_concat command itself? On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>> wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.**ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at><mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at><mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>>>>>wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.**mgh --o > /media/Dell/_FS/buckner_data/**** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:
> > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>>>wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/*** *subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as I press Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>**>. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**>.>**edu<greve@nmr.mgh.** harvard.edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>
> > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze: command failed: mri_concat > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though those files are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.****edu/pipermail/freesurfer/**2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://** mail.nmr.mgh.harvard.edu/**pipermail/freesurfhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-****stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/****fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/****subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/****mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________****_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > >>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>.>****harvard.edu <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><**Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<https://mail.nmr.**mgh.harvard.edu/mailman/**listinfo/freesurferhttps://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 greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>**>. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**>.>**edu<greve@nmr.mgh.** harvard.edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > >>> > > >>> > > >>> Phone Number: 617-724-2358 > > >>> Fax: 617-726-7422 > > >>> > > >>> Bugs: > > >>> surfer.nmr.mgh.harvard.edu/****fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> > >>> .nmr.mgh.harvard.edu/fswiki/**BugReportinghttp://nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://nmr.mgh.harvard.edu/fswiki/BugReporting
<http://nmr.mgh.harvard.edu/**fswiki/BugReporting<http://nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://nmr.mgh.harvard.edu/**fswiki/BugReporting http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harva** rd.edu/fswiki/**BugReporting http://harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/****BugReportinghttp://harvard.edu/fswiki/**BugReporting
<http://harvard.edu/fswiki/****BugReporting<http://harvard.edu/fswiki/**BugReporting>> <http://harvard.edu/fswiki/****BugReporting<http://harvard.edu/fswiki/**BugReporting><htt
> > >>> > p://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/****facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.** edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
<http://w
> > >>> ww.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://ww.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://ww.nmr.mgh.harvard.** edu/facility/filedrop/index.**htmlhttp://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>> > <http://www.nmr.mgh.harvard.****edu/facility/filedrop/index.****ht > > >>> > ml<http://www.nmr.mgh.harvard.** edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.****edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.** edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >>> > > >>> ______________________________****_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>.>****harvard.edu <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><**Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/****freesurfe > > >>> > r<https://mail.nmr.mgh.** harvard.edu/mailman/listinfo/**freesurferhttps://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<http://www.partners.org/**complianceline><http://www.**partners.or http://www.partners.or > > >>> g/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. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: > > > surfer.nmr.mgh.harvard.edu/****fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting><http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting>> <http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting>FileDrop: > > > www.nmr.mgh.harvard.edu/****facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.** edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> > > h.harvard.edu/facility/**filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/**facility/filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html><http://h.harvard.edu/**facility/filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html>> <http://h.harvard.edu/**facility/filedrop/index.htmlhttp://h.harvard.edu/facility/filedrop/index.html
Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.****edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.** edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna
Sorry for insisting Doug, but could you suggest how I can make mri_concat work at the command line, as it seems that this is at the core of QDEC's error. Note that I was previously able to run QDEC with the tutorial data, even though I did get this error then too, but it (seemingly) randomly went away after a few tries. mri_concat is the only FS command that returns me the command line after I type it and hit Enter.
cheers Tudor
On 29 March 2013 19:20, Tudor Popescu tudor3@gmail.com wrote:
Not sure what you mean .. Since I'm on Windows, without access to a Linux machine, I have to run it through Virtualbox.
It's strange how all other FS commands seem to work, but mri_concat is the only one that returns me straight to the command line. Could it have somehow become corrupt (although I can't think why that would have happened)?
On 29 March 2013 19:17, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Do you know if that version works outside of Virtualbox?
On 03/29/2013 03:13 PM, Tudor Popescu wrote:
I'm running freesurfer-Linux-centos4-**stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is 1.4 THanks for your help
On 29 March 2013 17:33, Douglas N Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on? On 03/28/2013 04:17 PM, Tudor Popescu wrote: I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt. The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz Could this indicate something is wrong with the mri_concat command itself? On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>> wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshotattached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com> > <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.**ac.atn0642496@students.meduniwien.ac.at <mailto:n0642496@students.**meduniwien.ac.atn0642496@students.meduniwien.ac.at
<mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at><mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>>>>>wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.**mgh --o > /media/Dell/_FS/buckner_data/**** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu><mailto:
> > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>>>>wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/*** *subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as I press Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>**>. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**>.>**edu<greve@nmr.mgh.** harvard.edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>
> > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze: command failed: mri_concat > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/****subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though those files are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.****edu/pipermail/freesurfer/**2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://** mail.nmr.mgh.harvard.edu/**pipermail/freesurfhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-****stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/****fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/****subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/****mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________****_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > >>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>.>****harvard.edu <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><**Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<https://mail.nmr.**mgh.harvard.edu/mailman/**listinfo/freesurferhttps://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 greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>**>. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard**>.>**edu<greve@nmr.mgh.** harvard.edu greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>
> > >>> > > >>> > > >>> Phone Number: 617-724-2358 > > >>> Fax: 617-726-7422 > > >>> > > >>> Bugs: > > >>> surfer.nmr.mgh.harvard.edu/****fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> > >>> .nmr.mgh.harvard.edu/fswiki/**BugReportinghttp://nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://nmr.mgh.harvard.edu/fswiki/BugReporting
<http://nmr.mgh.harvard.edu/**fswiki/BugReporting<http://nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://nmr.mgh.harvard.edu/**fswiki/BugReporting http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harva** rd.edu/fswiki/**BugReporting http://harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/****BugReportinghttp://harvard.edu/fswiki/**BugReporting
<http://harvard.edu/fswiki/****BugReporting<http://harvard.edu/fswiki/**BugReporting>> <http://harvard.edu/fswiki/****BugReporting<http://harvard.edu/fswiki/**BugReporting><htt
> > >>> > p://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/****facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.** edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
<http://w
> > >>> ww.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://ww.nmr.mgh.harvard.**edu/facility/filedrop/index.**html http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://ww.nmr.mgh.harvard.** edu/facility/filedrop/index.**htmlhttp://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>> > <http://www.nmr.mgh.harvard.****edu/facility/filedrop/index.****ht > > >>> > ml<http://www.nmr.mgh.harvard.** edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.****edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.** edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >>> > > >>> ______________________________****_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>.>****harvard.edu <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><**Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.****edu/mailman/listinfo/****freesurfe > > >>> > r<https://mail.nmr.mgh.** harvard.edu/mailman/listinfo/**freesurferhttps://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<http://www.partners.org/**complianceline><http://www.**partners.or http://www.partners.or > > >>> g/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. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: > > > surfer.nmr.mgh.harvard.edu/****fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/**fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting><http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting>> <http://arvard.edu/fswiki/**BugReporting<http://arvard.edu/fswiki/BugReporting>FileDrop: > > > www.nmr.mgh.harvard.edu/****facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**html http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.** edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.**edu/**facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> > > h.harvard.edu/facility/**filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/**facility/filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html><http://h.harvard.edu/**facility/filedrop/index.html<http://h.harvard.edu/facility/filedrop/index.html>> <http://h.harvard.edu/**facility/filedrop/index.htmlhttp://h.harvard.edu/facility/filedrop/index.html
Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.****edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.** edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > Hi surfers, > > sorry to bump this, but i seem to have theexact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna
Hi Tudor, if I knew I would certainly tell you! I think it must be a VB problem, which is beyond my skill. Maybe Nick or Zeke can help you. doug
On 3/31/13 6:57 PM, Tudor Popescu wrote:
Sorry for insisting Doug, but could you suggest how I can make mri_concat work at the command line, as it seems that this is at the core of QDEC's error. Note that I was previously able to run QDEC with the tutorial data, even though I did get this error then too, but it (seemingly) randomly went away after a few tries. mri_concat is the only FS command that returns me the command line after I type it and hit Enter.
cheers Tudor
On 29 March 2013 19:20, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
Not sure what you mean .. Since I'm on Windows, without access to a Linux machine, I have to run it through Virtualbox. It's strange how all other FS commands seem to work, but mri_concat is the only one that returns me straight to the command line. Could it have somehow become corrupt (although I can't think why that would have happened)? On 29 March 2013 19:17, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Do you know if that version works outside of Virtualbox? On 03/29/2013 03:13 PM, Tudor Popescu wrote: I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is 1.4 THanks for your help On 29 March 2013 17:33, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on? On 03/28/2013 04:17 PM, Tudor Popescu wrote: I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt. The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz Could this indicate something is wrong with the mri_concat command itself? On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>>> wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>>> > <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>>>>> wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "\" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.mgh --o > /media/Dell/_FS/buckner_data/** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>><mailto: > > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>> wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as I press Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>> > > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze: command failed: mri_concat > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though those files are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-**stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/**fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/**subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________**_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>.>**harvard.edu <http://harvard.edu> <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer > > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> > <http://harvard.edu/fswiki/**BugReporting><htt > > >>> > p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://w > > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > >>> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht > > >>> > ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > >>> > > >>> ______________________________**_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>.>**harvard.edu <http://harvard.edu> <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe > > >>> > r<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<http://www.partners.or > > >>> g/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. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.h > > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> > <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://www.nmr.mg > > > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> > <http://h.harvard.edu/facility/filedrop/index.html>> Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna
Hi Tudor,
I dont know why your having issues with the mri_concat binary in the Virtualbox environment. Ive never heard anyone having this issue before. Since that is the only FS command appears to not be working for you, I am strongly suspicious that somehow that file got corrupted. I am going to send you a copy if the mri_concat binary that you can put in your $FREESURFER_HOME/bin directory and overwrite the existing binary you currently have now (which doesnt work). You may want to save a copy of the original just in case.
-Zeke
Hi Tudor, if I knew I would certainly tell you! I think it must be a VB problem, which is beyond my skill. Maybe Nick or Zeke can help you. doug
On 3/31/13 6:57 PM, Tudor Popescu wrote:
Sorry for insisting Doug, but could you suggest how I can make mri_concat work at the command line, as it seems that this is at the core of QDEC's error. Note that I was previously able to run QDEC with the tutorial data, even though I did get this error then too, but it (seemingly) randomly went away after a few tries. mri_concat is the only FS command that returns me the command line after I type it and hit Enter.
cheers Tudor
On 29 March 2013 19:20, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
Not sure what you mean .. Since I'm on Windows, without access to a Linux machine, I have to run it through Virtualbox. It's strange how all other FS commands seem to work, but mri_concat is the only one that returns me straight to the command line. Could it have somehow become corrupt (although I can't think why that would have happened)? On 29 March 2013 19:17, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Do you know if that version works outside of Virtualbox? On 03/29/2013 03:13 PM, Tudor Popescu wrote: I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is1.4 THanks for your help
On 29 March 2013 17:33, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on? On 03/28/2013 04:17 PM, Tudor Popescu wrote: I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt. The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -otest.nii.gz
Could this indicate something is wrong with the mri_concat command itself? On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>>>wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com>>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at>> > <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at>
<mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>>>>> wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "\" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.mgh --o > /media/Dell/_FS/buckner_data/** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>><mailto: > > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>> wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as Ipress Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard>>. > <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard mailto:greve@nmr.mgh.harvard>>.>**edu<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>> > > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze:command failed: mri_concat > > >>> > > >>>
/media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>> thickness.fwhm10.fsaverage.mgh > > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though thosefiles are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2008-* > > >>> * > > >>> > > >>> > October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf > > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Any help greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-**stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/**fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/**subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________**_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > > >>> <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh>>.>**harvard.edu http://harvard.edu http://harvard.edu http://harvard.edu > http://harvard.edu<Freesurfer@nmr.mgh.har > > >>> vard.edu http://vard.edu http://vard.edu http://vard.edu http://vard.edu>
> > >>> > > >>> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>.>**edu<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer > > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> > <http://harvard.edu/fswiki/**BugReporting><htt > > >>> > p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://w > > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > >>> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht > > >>> > ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > >>> > > >>> ______________________________**_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>.>**harvard.edu <http://harvard.edu> <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe > > >>> > r<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<http://www.partners.or > > >>> g/complianceline>. If the e-mail was sent to you in > error > > >>> but does not containpatient information, > please contact the > > >>> sender and properly > > >>> dispose of the e-mail. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.h > > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> > <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html><http://www.nmr.mg > > > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> > <http://h.harvard.edu/facility/filedrop/index.html>> Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Zeke,
Thanks very much for this, I replaced the file with the one you sent, but now after typing a test command: mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz or indeed after typing mri_concat on its own, I always get the message "Killed" at the command line!
Tudor
On 1 April 2013 13:57, zkaufman@nmr.mgh.harvard.edu wrote:
Hi Tudor,
I dont know why your having issues with the mri_concat binary in the Virtualbox environment. Ive never heard anyone having this issue before. Since that is the only FS command appears to not be working for you, I am strongly suspicious that somehow that file got corrupted. I am going to send you a copy if the mri_concat binary that you can put in your $FREESURFER_HOME/bin directory and overwrite the existing binary you currently have now (which doesnt work). You may want to save a copy of the original just in case.
-Zeke
Hi Tudor, if I knew I would certainly tell you! I think it must be a VB problem, which is beyond my skill. Maybe Nick or Zeke can help you. doug
On 3/31/13 6:57 PM, Tudor Popescu wrote:
Sorry for insisting Doug, but could you suggest how I can make mri_concat work at the command line, as it seems that this is at the core of QDEC's error. Note that I was previously able to run QDEC with the tutorial data, even though I did get this error then too, but it (seemingly) randomly went away after a few tries. mri_concat is the only FS command that returns me the command line after I type it and hit Enter.
cheers Tudor
On 29 March 2013 19:20, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
Not sure what you mean .. Since I'm on Windows, without access to a Linux machine, I have to run it through Virtualbox. It's strange how all other FS commands seem to work, but mri_concat is the only one that returns me straight to the command line. Could it have somehow become corrupt (although I can't think why that would have happened)? On 29 March 2013 19:17, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Do you know if that version works outside of Virtualbox? On 03/29/2013 03:13 PM, Tudor Popescu wrote: I'm running freesurfer-Linux-centos4-stable-pub-v5.1.0, on Windows XP SP3, through Virtualbox 4.2.10. QDEC version is1.4 THanks for your help
On 29 March 2013 17:33, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: If yyou just type mri_concat at the command line and nothting happens, then something is definitely wrong. What system are you running on? On 03/28/2013 04:17 PM, Tudor Popescu wrote: I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt. The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -otest.nii.gz
Could this indicate something is wrong with the mri_concat command itself? On 28 March 2013 20:01, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: > Still stuck with this error in my QDEC analysis attempt, at my wit's > end, could anyone help please? Thanks! > Tudor > > On 26 March 2013 20:35, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>> > <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com <mailto:tudor3@gmail.com>>>>>wrote: > > Just giving this thread a new bump, as /again /I am receiving this > error from mri_concat, upon pressing the Analyze button in QDEC. > Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and > includes a copy of the fsaverage folder) and all files included in > the error are at the expected path. Screenshot attached. > > > On 18 March 2013 11:20, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com>> > <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com mailto:tudor3@gmail.com <mailto:tudor3@gmail.com mailto:tudor3@gmail.com>>>> wrote: > > Hi Andreas > > I don't think it's about the OS (I'm on WInXP SP3, 32 bit, > hosting Linux using Vritualbox), but about the environment > variables, even though from what I could see, I had them all > correctly set. I gave up and am just running this through FSL.. > > Tudor > > > On 18 March 2013 11:13, Andreas Berger > <n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at>> > <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at mailto:n0642496@students.meduniwien.ac.at>
<mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at> <mailto:n0642496@students.meduniwien.ac.at <mailto:n0642496@students.meduniwien.ac.at>>>>> wrote: > > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and > so did the full > > one. I think I initially had a "\" at the end of my > command, just after the > > file name, which should not have been there; although > having tried again > > with the backslash reinstated at the end, the command > still worked. Also, > > the Analyze in the QDEC GUI now completes without error > as well. > > > > It's quite frustrating that I still don't know why it > hasn't been working > > all this time, especially since I didn't really do > anything different now > > (that I was aware of!) and the files were located on the > same partition > > (Virtualbox's shared folder). > > > > Anyhow, thanks again for your kind help! > > > > Tudor > > > > On 31 January 2013 20:36, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > > >> Hi Doug, > > >> > > >> I'm not sure why that does not make sense, shouldn't > the input of > > >> mri_concat be several to-be-concatenated files rather > than a single > > >> file? > > > > > > Sorry, I did not mean to imply that the command line > was wrong, rather > > > that the behavior did not make sense -- it should > print *something* to > > > the terminal. It does make sense to have multiple > files, but it will > > > also work with a single file. I just suggested this to > make things > > > simpler. > > > > > >> Anyway, after trying out the command with only one of > the files from the > > >> tutorial, > > >> > > >> /mri_concat --debug > > >> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* > > >> *thickness.fwhm10.fsaverage.mgh --o > /media/Dell/_FS/buckner_data/** > > >> subjects/qdec/y.mgh/ > > >> > > >> > > >> ..the same thing happens, namely it returns to the > command prompt, with > > >> no message whatsoever. > > >> > > >> What could be wrong? As I mentioned, all those MGH > files are at the > > >> expected path. Thanks again for your help! > > > > > > What happens if you type mri_concat with no options at > all? > > > > > >> Tudor > > >> > > >> > > >> On 20 December 2012 05:24, Douglas Greve > > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>><mailto: > > >> > > >> greve@nmr.mgh.harvard.**edu > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>> wrote: > > >> That does not make sense. Try using only one > input file. Also, put > > >> --debug as the first option. > > >> doug > > >> > > >> On 12/19/12 8:32 AM, Tudor Popescu wrote: > > >>> Hi Doug, > > >>> So the full command is > > >>> > > >>> mri_concat > > >>> /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/130/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/039/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/123/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/095/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/067/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/004/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/133/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/097/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/073/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/149/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/045/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/136/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/144/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/032/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/131/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/145/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/111/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/102/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/074/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/114/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/008/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/128/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/099/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> --o > > >>> > /media/Dell/_FS/buckner_data/**subjects/qdec/lh-thickness-** > > >>> > > >>> age-fwhm10/y.mgh > > >>> > > >>> --debug > > >>> > > >>> ..however, as soon as Ipress Enter, I'm just > taken to the > > >>> command prompt again, with no output whatsoever! > Am I calling > > >>> mri_concat wrongly?! > > >>> > > >>> Tudor > > >>> > > >>> On 18 December 2012 17:15, Douglas N Greve > > >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard
<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>.>**edu<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>>> > > >>> > > >>> wrote: > > >>> Hi Tudor, > > >>> Can you run mri_concat from the command line > with the --debug > > >>> option > > >>> first. Send us the FULL command line and the > full terminal > > >>> output. > > >>> doug > > >>> > > >>> On 12/18/2012 09:35 AM, Tudor Popescu wrote: > > >>> > Hello everyone, > > >>> > > > >>> > I tried doing the QDEC group analysis > tutorial, however > > >>> > > >>> after doing > > >>> > > >>> > everything as instructed in the tutorial, > when pressing > > >>> > > >>> Analyze I get > > >>> > > >>> > the error message: > > >>> > > > >>> > /Error in Analyze:command failed: mri_concat > > >>> > > >>>
/media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** > > >>> > > >>>thickness.fwhm10.fsaverage.mgh
> > >>> > > >>> > (..)/ > > >>> > > > >>> > ..even though thosefiles are all > accessible there! I > > >>> > > >>> pasted that same > > >>> > > >>> > mri_concat manually into the terminal, > however no output is > > >>> > > >>> produced > > >>> > > >>> > at the command prompt, nor any files are > created. > > >>> > > > >>> > In previous attempts, I used to also get > this error > > >>> > > > >>> > /" .ERROR: QdecProject::VerifySubjects: > Couldn't find > > >>> > > >>> subject '032' in > > >>> > > >>> > SUBJECTS_DIR "/ > > >>> > /Syntax error: Bad fd number"/ > > >>> > > > >>> > after following the sh/bash workaround > from this > > >>> > > >>> > <https://mail.nmr.mgh.harvard.
**edu/pipermail/freesurfer/2008-*
> > >>> * > > >>> > > >>> > October/008618.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurf
> > >>> er/2008-October/008618.html> > > >>> > > >>> >previous > > >>> > > > >>> > thread, I no longer get that error, > however get stuck with > > >>> > > >>> the error > > >>> > > >>> > mentioned above. > > >>> > > > >>> > My SUBJECTS_DIR already contains a copy of > the default > > >>> > > >>> subjects folder. > > >>> > > >>> > Debug info below. Anyhelp greatly > appreciated! > > >>> > Tudor > > >>> > > > >>> > -------- > freesurfer-Linux-centos4-**stable-pub-v5.1.0 > > >>> > -------- Setting up environment for > FreeSurfer/FS-FAST (and > > >>> > FSL) FREESURFER_HOME > /home/virtualuser/freesurfer > > >>> > FSFAST_HOME > /home/virtualuser/freesurfer/**fsfast > > >>> > FSF_OUTPUT_FORMAT nii.gz > > >>> > SUBJECTS_DIR > /media/Dell/_FS/buckner_data/**subjects > > >>> > MNI_DIR /home/virtualuser/freesurfer/**mni > > >>> > > > >>> > > > >>> > > > >>> > > ______________________________**_________________ > > >>> > Freesurfer mailing list > > >>> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > > >>> <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh>>. > <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh mailto:Freesurfer@nmr.mgh>>.>**harvard.edu http://harvard.edu http://harvard.edu http://harvard.edu > http://harvard.edu<Freesurfer@nmr.mgh.har > > >>> vard.edu http://vard.edu http://vard.edu http://vard.edu http://vard.edu>
> > >>> > > >>> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > > >>> > > >>> > freesurfer<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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > >>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard<mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>. > <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard> <mailto:greve@nmr.mgh.harvard <mailto:greve@nmr.mgh.harvard>>>.>**edu<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><> > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting> <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> <http://harvard.edu/fswiki/**BugReporting> > <http://harvard.edu/fswiki/**BugReporting><htt > > >>> > p://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > > >>> FileDrop: > > >>> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E
<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E
<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E
> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E<http://w
> > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://ww.nmr.mgh.harvard.edu/facility/filedrop/index.html > > >>> > <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**ht
> > >>> > ml<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html%3E
> > >>> > > >>> > > >>> Outgoing: > > >>> > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
> > >>> > > >>> greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> > >>> > > >>> ______________________________**_________________ > > >>> Freesurfer mailing list > > >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > >>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>. > <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>>>.>**harvard.edu <http://harvard.edu> <http://harvard.edu> <http://harvard.edu> > <http://harvard.edu><Freesurfer@nmr.mgh.har > > >>> vard.edu <http://vard.edu> <http://vard.edu> <http://vard.edu> <http://vard.edu>> > > >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe
> > >>> > r<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
> > >>> > > >>> > > >>> 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<> > >>> g/complianceline>. If the e-mail was sent to you in > error > > >>> but does not containpatient information, > please contact the > > >>> sender and properly > > >>> dispose of the e-mail. > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><> > > arvard.edu/fswiki/BugReporting <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> <http://arvard.edu/fswiki/BugReporting> > <http://arvard.edu/fswiki/BugReporting>> FileDrop: > > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E
<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E
<http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E
> <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html%3E< http://www.nmr.mg
> > > h.harvard.edu/facility/filedrop/index.html <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> <http://h.harvard.edu/facility/filedrop/index.html> > <http://h.harvard.edu/facility/filedrop/index.html>> Outgoing: > > > > ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
> greve/ > > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> > Hi surfers, > > sorry to bump this, but i seem to have the exact same problem: > > - qdec informs me that mri_concat failed > - mri_concat itself produces no output at all > - also not with --debug or without any arguments at all > - however, mri_concat has a non-zero exit status > > btw, i also ran into the sh syntax error, which i worked > around by linking sh > to bash. i assume this is not directly related, but maybe > Tudor and i share > the same platform, to which both problems are related? > > i am using the 32bit centOS4 build on debian 7. > > > greetings from Vienna
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.
Hi Tudor,
That is unfortunate. You mention in the email below dated (Feb 1) that you got mri_concat working for you. If it worked for you then, but doesnt now, and nothing changed in the meantime, Im not sure there's much we can do to diagnose the issue. The mri_concat binary I sent you works in our CentOS4 environment and as well as the countless others who have downloaded freesurfer 5.1 for CentOS4. Are you required to use 5.1 for your analysis? Freesurfer 5.2 was released earlier this month and can be downloaded here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
Hi Zeke,
Thanks very much for this, I replaced the file with the one you sent, but now after typing a test command: mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz or indeed after typing mri_concat on its own, I always get the message "Killed" at the command line!
Tudor
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error from mri_concat while using QDEC From: "Tudor Popescu" tudor3@gmail.com Date: Fri, February 1, 2013 12:12 pm To: "Douglas N Greve" greve@nmr.mgh.harvard.edu Cc: "free surfer" freesurfer@nmr.mgh.harvard.edu --------------------------------------------------------------------------
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
Thanks Zeke. I tried upgrading to the latest FS version, 5.2.0, but I see that the available download ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Linux-centos4-stable-pub-v5.2.0.tar.gzis only in .tar.fz format rather than in .VDI format, as v5.1.0ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdiwas (and the .TAR archive does not contain a .VDI file inside it). Virtualbox seems to only accept the VDI format. Apologies if there's something obvious here that I"m not seeing..
And yes, it's true that I eventually did get mri_concat to work in QDEC, however that was only after repeatedly trying the same thing, I hadn't really changed anything. My guess is that, when I used to get that error from QDEC/mri_concat in the past, it was another case of mri_concat not responding to the command line. This could be, as Doug says, a problem with my Virtualbox, but unfortunately I don't know what else to do with it, and I've been wanting to complete this analysis for weeks now... :(
On 1 April 2013 15:24, zkaufman@nmr.mgh.harvard.edu wrote:
Hi Tudor,
That is unfortunate. You mention in the email below dated (Feb 1) that you got mri_concat working for you. If it worked for you then, but doesnt now, and nothing changed in the meantime, Im not sure there's much we can do to diagnose the issue. The mri_concat binary I sent you works in our CentOS4 environment and as well as the countless others who have downloaded freesurfer 5.1 for CentOS4. Are you required to use 5.1 for your analysis? Freesurfer 5.2 was released earlier this month and can be downloaded here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
Hi Zeke,
Thanks very much for this, I replaced the file with the one you sent, but now after typing a test command: mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz or indeed after typing mri_concat on its own, I always get the message "Killed" at the command line!
Tudor
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error from mri_concat while using QDEC From: "Tudor Popescu" tudor3@gmail.com Date: Fri, February 1, 2013 12:12 pm To: "Douglas N Greve" greve@nmr.mgh.harvard.edu Cc: "free surfer" freesurfer@nmr.mgh.harvard.edu
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
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.
Hi Zeke, was wondering if you saw my message. VirtualBox only seems to accept VDI files, so it seems I cannot make use of the new 5.2 version, which is downloadable only as a .TAR.GZ Sorry this is proving so difficult.. T
On 1 April 2013 15:29, Tudor Popescu tudor3@gmail.com wrote:
Thanks Zeke. I tried upgrading to the latest FS version, 5.2.0, but I see that the available download ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Linux-centos4-stable-pub-v5.2.0.tar.gzis only in .tar.fz format rather than in .VDI format, as v5.1.0ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdiwas (and the .TAR archive does not contain a .VDI file inside it). Virtualbox seems to only accept the VDI format. Apologies if there's something obvious here that I"m not seeing..
And yes, it's true that I eventually did get mri_concat to work in QDEC, however that was only after repeatedly trying the same thing, I hadn't really changed anything. My guess is that, when I used to get that error from QDEC/mri_concat in the past, it was another case of mri_concat not responding to the command line. This could be, as Doug says, a problem with my Virtualbox, but unfortunately I don't know what else to do with it, and I've been wanting to complete this analysis for weeks now... :(
On 1 April 2013 15:24, zkaufman@nmr.mgh.harvard.edu wrote:
Hi Tudor,
That is unfortunate. You mention in the email below dated (Feb 1) that you got mri_concat working for you. If it worked for you then, but doesnt now, and nothing changed in the meantime, Im not sure there's much we can do to diagnose the issue. The mri_concat binary I sent you works in our CentOS4 environment and as well as the countless others who have downloaded freesurfer 5.1 for CentOS4. Are you required to use 5.1 for your analysis? Freesurfer 5.2 was released earlier this month and can be downloaded here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
Hi Zeke,
Thanks very much for this, I replaced the file with the one you sent,
but
now after typing a test command: mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz or indeed after typing mri_concat on its own, I always get the message "Killed" at the command line!
Tudor
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error from mri_concat while using QDEC From: "Tudor Popescu" tudor3@gmail.com Date: Fri, February 1, 2013 12:12 pm To: "Douglas N Greve" greve@nmr.mgh.harvard.edu Cc: "free surfer" freesurfer@nmr.mgh.harvard.edu
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
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