Hi Bruce, trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also attaching dmrirc files. Thank you very much.
Stefano
----Messaggio originale---- Da: fischl@nmr.mgh.harvard.edu Data: 1-mag-2013 15.39 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu, ayendiki@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplete tracts
Hi Stefano
you need to tell us what command you were running.
cheers Bruce
On Wed, 1 May 2013, stdp82@virgilio.it wrote:
I have this error:
writing registered surface
to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av
g35.sphere.reg... expanding nbhd size to 1 1109: 1 negative triangles mris_resample: Command not found.
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 30-apr-2013 21.12 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: incomplete tracts
Like I said in my previous email to you, please do not specify the CVS template. This means delete the cvstempdir line from your configuration file, or comment it out.
On Tue, 30 Apr 2013, stdp82@virgilio.it wrote:
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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > The information in this e-mail is intended only for the person
to
whom
it is
> > addressed. If you believe this e-mail was sent to you in error
and
the
> > contains patient information, please contact the Partners
Compliance
HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was
sent to
you
in error
> > but does not contain patient information, please contact the
sender
and properly
> > dispose of the e-mail. > > > > > > > > > > -- > > http://gerit-orientation.blogspot.com > > http://team-arzgebirg.blogspot.com > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >
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