yes, I tried.
I'm attacking the last configuration file that I used.
Stefano
----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 9-apr-2013 1.42
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] incomplete tracts
What registration methods are you using for the intra-subject and
inter-subject registration? Have you tried the different options?
On Fri, 5 Apr 2013, stdp82@virgilio.it wrote:
> Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor.
>
> ----Messaggio originale----
> Da: ayendiki@nmr.mgh.harvard.edu
> Data: 5-apr-2013 18.57
> A: <stdp82@virgilio.it>
> Cc: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts
>
>
> What you say "again" you mean with 5.2?
>
> On Fri, 5 Apr 2013, stdp82@virgilio.it wrote:
>
> > Hi Anastasia,
> > yes, for some subject the low-b volume is in the end.
> > Some subjects have again incomplete tracts.
> > I'm attacking an example of configuration file that I'm using.
> > I hope that you can check it please.
> >
> > Thanks,
> >
> >
> > Stefano
> >
> > ----Messaggio originale----
> > Da: ayendiki@nmr.mgh.harvard.edu
> > Data: 5-apr-2013 18.45
> > A: <stdp82@virgilio.it>
> > Cc: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>
> > Ogg: Re: R: Re: [Freesurfer] incomplete tracts
> >
> >
> > Hi Stefano - In your case we determined that the ones that had the low-b
> > volume in the end didn't run correctly, right? In that case, I didn't need
> > to see anything, you were going to try running 5.2.
> >
> > a.y
> >
> > On Fri, 5 Apr 2013, stdp82@virgilio.it wrote:
> >
> > > Hi Anastasia,
> > > could I send you the data of a subject that I don't run correctly?
> > >
> > > I still have some subjects with tracts incomplete and I do not know if
> it depends
> > from
> > > my analysis or whether the images are not good.
> > >
> > > Thanks,
> > >
> > >
> > > Stefano
> > >
> > >
> > > ----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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> > > >
> > > >
> > > >
> > > >
> > > >
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> > > >
> > > > --
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> > > >
> > > >
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