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<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/BugReporting<http://surfer.nmr.mgh.h
> > arvard.edu/fswiki/BugReporting> FileDrop:
> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://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