Are you running this on your own subject or the tutorial subject?

Please include the freesurfer list on all emails with tracula questions.

Thanks, a.y

On Tue, 9 Apr 2013, Gerit Pfuhl wrote:

Dear Anastasia,

I got some improvement by setting nctps to 7 (as I had done last week with version 5.1.0). Now, we installed freesurfer 5.2.0 and I rerun one subject (changed drmirc file) but I got the following message: niiRead(): error opening file /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz ERROR: Could not read /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz

diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz does not exist, so that must be a new data set.??? Though I saw that the diffusion_tutorial page is from Sep 2012.

Regards Gerit

On 5 April 2013 18:23, Gerit Pfuhl gerit.pfuhl@gmail.com wrote: Hi Anastasia,

I will know more on monday, Then  should also be able to upload files.

Bests Gerit

On 5 April 2013 17:37, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Hi Gerit - If it's not an issue with the gradient table but instead a tractography initialization issue, I strongly recommend
  running 5.2 with bbregister for the registration (which is the default in 5.2 anyway).

  You can also upload an example data set with issues (include: dmri, dmri.bedpostX, dlabel, dpath, scripts) here for me to take a
  look:
          https://gate.nmr.mgh.harvard.edu/filedrop2/

  Hope this helps,
  a.y

  On Fri, 5 Apr 2013, Gerit Pfuhl wrote:

        Dear Anastasia,

        thanks for the help. There is also a line option in freeview. However we still have
        brains with missing tracks, I rerun them with increasing the ncpts and registering to
        bbr (since that is default in Tracula 5.2.). We are reasonable confident that our bvel
        and bvac are correct, since we have roughly 20 cases out of 90 processed brains where
        there are no missing tracts. Further sometimes only one tract is missing, sometimes it
        is more severe. We could not find any correlation with recon-all problems or DTI raw
        data issues (all but one were without moving artefacts). Since we are running bedpostx
        outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an issue
        that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0?
        I guess we need to change the dcmrirc files only a bit.

        Kind regards
        Gerit Pfuhl


        On 3 April 2013 16:59, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

              Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus
              callosum follow the curvature of the corpus callosum, and in a sagittal
              view to see if the lines in the cingulum follow the curvature of the
              cingulum. Does this make sense?

              a.y

              On Wed, 3 Apr 2013, Roschinski, Benjamin wrote:

              Dear Anastasia,

              we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our
              gradient table is wrong but I am not really sure how to analyse
              these informations. You wrote to Stefano the lines have to point in
              the right direction and that the eigenvectors are not pointing along
              his corpus callosum. Can you give me a more detailed description
              what I have to do when I dislpay dtifit_V1 as lines, overlaid on
              dtifit_FA.

              Thanks and kind regards
              Benjamin

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