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>> 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>> 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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > 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> >> 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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto: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. >> >> > > -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
