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. >> >
dmrirc
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