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. >>>> >>> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
