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 <gr...@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 <gr...@nmr.mgh.harvard.edu<mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@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 >>> <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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/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:freesur...@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 >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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:freesur...@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 > gr...@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> > FileDrop: > 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/> > >
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