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