----Messaggio originale----
Da: ayendiki@nmr.mgh.harvard.edu
Data: 1-mag-2013 18.40
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] incomplete tracts
Hi Stefano - You'll have to include the log file, so that we can see the
exact command line that was being run when the error happened.
Thanks,
a.y
On Wed, 1 May 2013, stdp82@virgilio.it wrote:
> 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
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> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > 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
> > > > > > e-mail
> > > > > > > > > contains patient information, please contact the Partners
> > Compliance
> > > > > > HelpLine at
> > > > > > > > > http://www.partners.org/complianceline . If the e-mail was
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> > > > > you
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> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > http://gerit-orientation.blogspot.com
> > > > > > > > > http://team-arzgebirg.blogspot.com
> > > > > > > > >
> > > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > Freesurfer mailing list
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> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >_______________________________________________
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> > > >
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> >
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