I have this error:
writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_avg35.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
> > > > e-mail
> > > > > > > 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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >_______________________________________________
> > > > 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
> > > > e-mail
> > > > 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.
> > > >
> > > >
> > > >
> > > >_______________________________________________
> > > 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
> > > e-mail
> > > 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.
> > >
> > >
> > >
> > >_______________________________________________
> > 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 e-mail
> > 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.
> >
> >
> >
> >_______________________________________________
> 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 e-mail
> 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.
>
>
>
>_______________________________________________
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 e-mail
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.