----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 5-apr-2013 17.37
A: "Gerit Pfuhl"<gerit.pfuhl@gmail.com>
Cc: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] incomplete tracts

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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