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/**
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ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
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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<
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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