Re: [Freesurfer] Error from mri_concat while using QDEC

On 01/31/2013 12:30 PM, Tudor Popescu wrote:

Hi Doug,

I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file?

Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler.

Anyway, after trying out the command with only one of the files from the tutorial,

/mri_concat --debug /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/subjects/qdec/y.mgh/

..the same thing happens, namely it returns to the command prompt, with no message whatsoever.

What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help!

What happens if you type mri_concat with no options at all?

Tudor

On 20 December 2012 05:24, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

That does not make sense. Try using only one input file. Also, put
--debug as the first option.
doug






On 12/19/12 8:32 AM, Tudor Popescu wrote:

...

Hi Doug,
So the full command is

mri_concat
/media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/141/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/084/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/021/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/093/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/080/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/091/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/040/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/017/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/138/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/106/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/108/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/092/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/124/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/129/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/103/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/130/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/039/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/123/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/095/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/067/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/004/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/133/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/097/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/073/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/149/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/045/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/136/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/144/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/032/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/131/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/145/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/111/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/102/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/074/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/114/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/008/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/128/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/099/surf/lh.thickness.fwhm10.fsaverage.mgh
--o
/media/Dell/_FS/buckner_data/subjects/qdec/lh-thickness-age-fwhm10/y.mgh
--debug

..however, as soon as I press Enter, I'm just taken to the
command prompt again, with no output whatsoever! Am I calling
mri_concat wrongly?!

Tudor

On 18 December 2012 17:15, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Hi Tudor,
    Can you run mri_concat from the command line with the --debug
    option
    first. Send us the FULL command line and the full terminal
    output.
    doug



    On 12/18/2012 09:35 AM, Tudor Popescu wrote:
    > Hello everyone,
    >
    > I tried doing the QDEC group analysis tutorial, however
    after doing
    > everything as instructed in the tutorial, when pressing
    Analyze I get
    > the error message:
    >
    > /Error in Analyze: command failed: mri_concat
    >
    /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh
    >
    /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh
    > (..)/
    >
    > ..even though those files are all accessible there! I
    pasted that same
    > mri_concat manually into the terminal, however no output is
    produced
    > at the command prompt, nor any files are created.
    >
    > In previous attempts, I used to also get this error
    >
    > /" .ERROR: QdecProject::VerifySubjects: Couldn't find
    subject '032' in
    > SUBJECTS_DIR "/
    > /Syntax error: Bad fd number"/
    >
    > after following the sh/bash workaround from this
    >
    <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.html>previous
    > thread, I no longer get that error, however get stuck with
    the error
    > mentioned above.
    >
    > My SUBJECTS_DIR already contains a copy of the default
    subjects folder.
    >
    > Debug info below. Any help greatly appreciated!
    > Tudor
    >
    > -------- freesurfer-Linux-centos4-stable-pub-v5.1.0 --------
    > Setting up environment for FreeSurfer/FS-FAST (and FSL)
    > FREESURFER_HOME /home/virtualuser/freesurfer
    > FSFAST_HOME /home/virtualuser/freesurfer/fsfast
    > FSF_OUTPUT_FORMAT nii.gz
    > SUBJECTS_DIR  /media/Dell/_FS/buckner_data/subjects
    > MNI_DIR /home/virtualuser/freesurfer/mni
    >
    >
    >
    > _______________________________________________
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    --
    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

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