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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