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 <tud...@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 <tud...@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 < >> n0642...@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 <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/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:freesur...@nmr.mgh.**harvard.edu >>> <freesur...@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 >>> > >>> 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 >>> <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> >>> > >>> >>> > >>> >>> > >>> 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 >>> <freesur...@nmr.mgh.har >>> > >>> 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 >>> > > 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.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 >>> >> >> >
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