Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC?
On 03/28/2013 03:51 PM, Tudor Popescu wrote: > 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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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><mailto: > > >> > > >> gr...@nmr.mgh.harvard.**edu > <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> > > >>> <mailto:gr...@nmr.mgh.harvard. > <mailto:gr...@nmr.mgh.harvard.>**edu<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<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:Freesurfer@nmr.mgh.harvard.edu> > > >>> > > >>> <mailto:freesur...@nmr.mgh. > <mailto:freesur...@nmr.mgh.>**harvard.edu > <http://harvard.edu><freesur...@nmr.mgh.har > > >>> vard.edu <http://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> > > >>> <mailto:gr...@nmr.mgh.harvard. > <mailto:gr...@nmr.mgh.harvard.>**edu<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><http://surfer > > >>> .nmr.mgh.harvard.edu/fswiki/BugReporting > <http://nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >>> > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting > <http://harvard.edu/fswiki/**BugReporting><htt > > >>> > p://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://w > > >>> ww.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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:Freesurfer@nmr.mgh.harvard.edu> > > >>> <mailto:freesur...@nmr.mgh. > <mailto:freesur...@nmr.mgh.>**harvard.edu > <http://harvard.edu><freesur...@nmr.mgh.har > > >>> vard.edu <http://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 > <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><http://surfer.nmr.mgh.h > > > arvard.edu/fswiki/BugReporting > <http://arvard.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.mg > > > h.harvard.edu/facility/filedrop/index.html > <http://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 > > > > > > > _______________________________________________ > 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 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 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.
