Hi Gari - Just looked at your subject. The bottom of the brain is truncated in the DWIs. The slices stop in the middle of the angular bundle, which is why the -prior step failed in that pathway. But I expect there'd be problems with other tracts that reach that inferior, even if they didn't fail completely - corticospinal, uncinate, inferior longitudinal fasciculus.

a.y

On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:

Hi Anastasia,
I was  testing just with one subject and it finished the -prep part with
error.
Please find attached the trac-all.log file.
As this is a test user you will see some other invocations of trac-all. The
last build_stamp starts at row 54.500 aprox.
(just in case: I started new from de DICOMS and the dcm2nii, and I am using
the resulting .nii, .bvec and .bval, just in case I attached the dmrirc
too).

Thanks again for your help!
Gari


On Thu, Sep 26, 2013 at 8:01 AM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

      Hi Gari - Yes, that's your best option right now. Sorry for the
      inconvenience. I'll make sure to add the option to have one
      gradient file per subject in the next version.

      a.y

      On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:

            Hi! Thanks for the fast answer. If I do: diff
            id1.bvec id2.bvec
            I can see some clear differences. 

            I was told that in FSL I should use the bvecs and
            bvals created in dcm2nii
            per subject, so I understand I should do the same
            now?
            Do you think an option would be to script the
            creation of a dmrirc file per
            each subject and then launch as many trac-alls as
            subjects?

            Thanks again,
            Gari

            On Thursday, September 26, 2013, Anastasia Yendiki
            wrote:

                  Hi Gari - Sorry, right now the assumption is
            that the gradient
                  vectors are the same for all subjects. How
            different are they?

                  a.y

                  On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga
            wrote:

                        Hi Anastasia,I am setting up the dmrirc
            file to run
                        Tracula. I am using
                        Siemens Dicoms, so I did not specify any
            setting for
                        bval and bvec, but when
                        trac-all -prep starts running it gives
            the following
                        error: mv: cannot stat
                       
            'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs':
                        No such file or
                        directory

                        Ok, so I understand that our problem is
            that we
                        don't have MGH Siemens
                        Dicom. 

                        So I used dcm2nii to convert it to .nii
            files and
                        each conversion gives me a
                        SubjectID.bval and SubjectID.bvec. Every
            .bval is
                        the same file, but every
                        .bvec file is a different one. 

                        I can edit "set dcm_list = " to include
            all the
                        newly created .nii files,
                        but

                        My question is: 
                        - How can I specify every .bvec value
            for every
                        subject? In the dmrirc file
                        everything I see is a "set bvecfile = "
            option.

                        Thank you very much,
                        Gari




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