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. >>>>> >>>> >> >
trac-all.log
Description: Binary data
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