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 rspriti@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 ayendiki@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?
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