Re: [Freesurfer] TRACULA exited with errors

Hi Carolina - The bvecs file that you're attaching has commas as the decimal separator. See this suggestion: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18395.html

The input DWIs can be in a format other than dicom, but then some additional inputs must be specified, see: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

Also, from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula: Note that, because TRACULA relies on the underlying anatomy as derived from the FreeSurfer cortical parcellation and subcortical segmentation, these need to be generated before running trac-all. This means that before you run trac-all you will have to analyze your subjects' anatomical images with recon-all and make sure that they have a good-quality mri/aparc+aseg.mgz.

Hope this helps, a.y

On Mon, 2 Apr 2012, Carolina Valencia wrote:

I have under dmri folder of Diff001 2 files bvals and bvecs without an order of columns, in the same folder I found files called dwi_orig.mghdti.bvals andbvecs which have the rows and columns you said. I attached the files (I rename them to old in order to save the correct ones) Regarding the question to process my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right?

Thanks for the help!

2012/4/2 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Hi Carolina - The bvecs and bvals in the tutorial data should have 3 lines and 1 line, respectively, with 70 entries in
  each line. Is that not what you have?

  For different possibilities for inputs, please see the tracula wiki page, and particularly the link to the example dmrirc
  file:
         http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

  a.y

  On Mon, 2 Apr 2012, Carolina Valencia wrote:


        Hi FS users
        I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first
        command step trac-all
        -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject
        It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and
        chech the size.

        #@# Tensor fit lun abr  2 13:23:46 COT 2012
        dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m
        /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
        -r
        /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b
        /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o
        /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit
        Error: bvecs and bvals don't have the same number of entries
        Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012
        i686 GNU/Linux

        trac-preproc exited with ERRORS at lun abr  2 13:23:49 COT 2012

        Another question is related to process my own data. I have to recon-all my structural data and to have the
        orig DWI dicoms in order to
        use trac-all, right?

        Many thanks,

        Best regards
        --
        -- 
        Carolina Valencia M

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-- --  Carolina Valencia M