When I look at them with the more command on a linux machine, I see 2 lines in bval and 6 lines in bvec. Most likely this is a problem with the text files being created with a windows program like excel and not having unix-compatible end-of-line characters. It's been discussed a few times in the archives. You'll have to make sure you have text files that can be read properly on unix.
On Wed, 15 Feb 2012, Tetiana Dadakova wrote: > 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. >>>>>>>>> >>>>>>>> >>>>>> >>>>> >>>> >>> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
