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 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
>>
>>
>>
>

> _______________________________________________
> 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

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