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>

...

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    --
    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
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    person to whom it is
    addressed. If you believe this e-mail was sent to you in
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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/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/

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<

http://surfer

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<htt

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http://w

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**edu/facility/filedrop/index.**ht

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

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    The information in this e-mail is intended only for the
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...

...

    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

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<

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%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<

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

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><

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%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<

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%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 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

---

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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/

---

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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 . 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

...

<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<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/

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>

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        <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>
    <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>

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        >         <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>
    <mailto:n0642496@students.**meduniwien.ac.at<n0642496@students.meduniwien.ac.at>

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        <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>

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<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

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        >             > >>>     <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>

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>>

        >             > >>>
        >             > >>> 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

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        >             <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
    <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>

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        <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
    <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>

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        >             > >>>
        >             > >>>         <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

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        >             > >>>         <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

...

<http://surfer

        >             > >>>                   .

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

...

<http://surfer.**nmr.mgh.h 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>

...

        >             <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

...

<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<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

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>
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                    <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
                    >             > >>>
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        <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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                <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>>
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        <mailto:Freesurfer@nmr.mgh> <mailto:Freesurfer@nmr.mgh
        <mailto:Freesurfer@nmr.mgh>>>.
                    >             <mailto:Freesurfer@nmr.mgh
        <mailto:Freesurfer@nmr.mgh>
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        <mailto:Freesurfer@nmr.mgh>>
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        <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>>
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        <mailto:greve@nmr.mgh.harvard.edu>
                <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>>
                    >            
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
                <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>

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

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                    >             > >
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                    >                  
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                    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 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 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%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>>
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        <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
                    >
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        <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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        <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
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                <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<

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
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                    <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

...

...

                    >
        <

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...

...

                    >             > >
        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.

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

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