28 Mar
2013
28 Mar
'13
4:17 p.m.
I tried running it by itself, to remind me of the syntax, so that I can do a simple concatenation to see if it works. But after typing mri_concat and hitting Enter, nothing happens, I'm just returned to the command prompt.
The same happens if I type the following command, from the folder containing the two input files mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz
Could this indicate something is wrong with the mri_concat command itself?
On 28 March 2013 20:01, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 <tudor3@gmail.com mailto:tudor3@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 <tudor3@gmail.com <mailto:tudor3@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 <n0642496@students.meduniwien.ac.at <mailto:n0642496@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu><mailto: > >> > >> greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> > >>> <mailto:greve@nmr.mgh.harvard. <mailto:greve@nmr.mgh.harvard.>**edu<greve@nmr.mgh.harvard.edu
<mailto: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<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:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>**harvard.edu <http://harvard.edu><Freesurfer@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 > >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >>> <mailto:greve@nmr.mgh.harvard. <mailto:greve@nmr.mgh.harvard.>**edu<greve@nmr.mgh.harvard.edu
<mailto:greve@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><> >>> .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%3E<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%3E
> >>> > >>> > >>> 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:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>**harvard.edu <http://harvard.edu><Freesurfer@nmr.mgh.har > >>> vard.edu <http://vard.edu>> > >>> > >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfe
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> >>> > >>> > >>> 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<> >>> 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 > > greve@nmr.mgh.harvard.edu <mailto:greve@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><> > 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%3E< 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 sameproblem:
- 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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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.