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?

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!

Tudor

On 20 December 2012 05:24, Douglas Greve <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> 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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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