Sorry for bothering you again, I have another error now: "Error: bvecs and bvals don't have the same number of entries". Visually my bval/bvec files seem ok to me. I can't find the problem. I attach the files, could you please take a look on them?
Thank you very much, Tanja. On Tue, Feb 14, 2012 at 7:31 PM, Tetiana Dadakova <tetian...@gmail.com> wrote: > I see, thank you :) > > > On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> wrote: >> >> PS: The info on what you need to set it here: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc >> >> # Number of low-b images >> # Must be specified if inputs are not DICOM >> # Default: Read from DICOM header >> # >> set nb0 = 10 >> >> >> >> On Tue, 14 Feb 2012, Tetiana Dadakova wrote: >> >>> Dear Priti, Anastasia, >>> >>> Thank you for your help, I created bvec and bval files and it went fine. >>> But now I have another error in preprocessing step. >>> I attach a log file. Could you please take a look at that? >>> >>> Thank you, >>> Tanja. >>> >>> >>> >>> trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 >>> >>> >>> >>> >>> On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan >>> <rspr...@nmr.mgh.harvard.edu> wrote: >>>> >>>> Hi Tanja, >>>> >>>> Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs >>>> was created at all? It looks like that may not have been created and >>>> that's why it can't find "dwi_orig_flip.mghdti.bvecs". If your bvals and >>>> bvecs information is not encoded in the dicom header, then you can >>>> specify >>>> it explicitly in the dmrirc file. >>>> >>>> Please refer to the following page for instructions on how to specify >>>> your >>>> bvals and bvecs for tracula: >>>> >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>>> >>>> Hope this helps, >>>> Priti >>>> >>>> >>>>> Hi Priti, >>>>> >>>>> I changed the dmrirc file to the one you sent, but unfortunately got >>>>> the same error. I attach the log (although it is basically the same). >>>>> Do you have any ideas what else can cause it? >>>>> >>>>> Thanks again, >>>>> Tanja. >>>>> >>>>> On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan >>>>> <rspr...@nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> Hi Tanja, >>>>>> >>>>>> I think the problem may be due to the trailing slash you've included >>>>>> while >>>>>> specifying $dtroot, $SUBJECTS_DIR etc. >>>>>> >>>>>> >>>>>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ >>>>>> >>>>>> should be >>>>>> >>>>>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 >>>>>> >>>>>> >>>>>> trac-all usually adds the '/' and since you're adding an extra '/', >>>>>> it's >>>>>> giving an error. I've edited your dmrirc file and removed those >>>>>> trailing >>>>>> slashes. Could you run this again and let us know if it solves the >>>>>> problem? >>>>>> >>>>>> Hope this is helpful, >>>>>> Priti >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Thank you Priti and Anastasia, >>>>>>> >>>>>>> Anastasia, just wanted to clarify, I meant >>>>>>> $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for >>>>>>> this misunderstanding. >>>>>>> >>>>>>> I attach my configuration file and the command I use is < trac-all >>>>>>> -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc >>>>>>>> >>>>>>>> . >>>>>>> >>>>>>> I also attach a picture of my file tree and a track-all.log file. >>>>>>> >>>>>>> Thank you for your time and help, >>>>>>> Tanja. >>>>>>> >>>>>>> On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki >>>>>>> <ayend...@nmr.mgh.harvard.edu> wrote: >>>>>>>> >>>>>>>> >>>>>>>> Hi Tanja - The file is supposed to be created under >>>>>>>> $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as >>>>>>>> /dmri/bvecs, >>>>>>>> this means that something wasn't defined correctly. What is the exact >>>>>>>> trac-all command line that you're using? And your configuration file >>>>>>>> if >>>>>>>> you're using one? >>>>>>>> >>>>>>>> a.y >>>>>>>> >>>>>>>> >>>>>>>> On Thu, 2 Feb 2012, Tetiana Dadakova wrote: >>>>>>>> >>>>>>>>> Dear list, >>>>>>>>> >>>>>>>>> I try to run TRACULA pre-processing step and I get the following >>>>>>>>> error: /dmri/bvecs: No such file or directory. >>>>>>>>> >>>>>>>>> I have a folder with reconstructed T1 data and a folder with raw >>>>>>>>> dicom >>>>>>>>> DTI data. When I start trac-all -prep, it creates directory /dmri/, >>>>>>>>> but it doesn't create the bvecs file. >>>>>>>>> Should I create it myself using dcm2nii or is it supposed to be >>>>>>>>> created automatically? >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> Tanja. >>>>>>>>> _______________________________________________ >>>>>>>>> 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. >>>>>>>> >>>>>>> >>>>> >>>> >>> >>
bval
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bvec
Description: Binary data
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