Hi Anastasia,

when I run the configuration file (which I'm attaching)
ERROR: Could not find CVS template

I apologize but which is the correct directory of CVS template?

Thanks,


Stefano


----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 26-apr-2013 20.08
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re:  R: Re:  incomplete tracts


Hi Stefano - Just use the default for that, you don't need to specify the
location.

a.y

On Sun, 21 Apr 2013, stdp82@virgilio.it wrote:

> Hi Anastasia, 
> I apologize but I do not find CVS template? Where it should be located?
>
> Thank you very much,
>
>
> Stefano
>
>
>
> ----Messaggio originale----
> Da: ayendiki@nmr.mgh.harvard.edu
> Data: 9-apr-2013 17.50
> A: <stdp82@virgilio.it>
> Cc: <freesurfer@nmr.mgh.harvard.edu>
> Ogg: Re: [Freesurfer] R: Re:  incomplete tracts
>
>
> Hi Stefano - Did you try CVS for the inter-subject registration? It
> doesn't look like it from the configuration file.
>
> a.y
>
> On Tue, 9 Apr 2013, stdp82@virgilio.it wrote:
>
> > Hi Anastasia,
> > yes, I tried.I'm attacking the last configuration file that I used.
> >
> > Thanks, 
> >
> >
> > 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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> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > The information in this e-mail is intended only for the person to
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> > > > > >
> > > > > >
> > > > > > --
> > > > > > http://gerit-orientation.blogspot.com
> > > > > > http://team-arzgebirg.blogspot.com
> > > > > >
> > > > > >
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