No I did not try it. Now I'm trying to perform it.
Thanks, Stefano ----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 9-apr-2013 17.50 A: <std...@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, std...@virgilio.it wrote: > Hi Anastasia, > yes, I tried.I'm attacking the last configuration file that I used. > > Thanks, > > > Stefano > > ----Messaggio originale---- > Da: ayend...@nmr.mgh.harvard.edu > Data: 9-apr-2013 1.42 > A: <std...@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, std...@virgilio.it wrote: > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > > > ----Messaggio originale---- > > Da: ayend...@nmr.mgh.harvard.edu > > Data: 5-apr-2013 18.57 > > A: <std...@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, std...@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: ayend...@nmr.mgh.harvard.edu > > > Data: 5-apr-2013 18.45 > > > A: <std...@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, std...@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: ayend...@nmr.mgh.harvard.edu > > > > Data: 5-apr-2013 17.37 > > > > A: "Gerit Pfuhl"<gerit.pf...@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 > > <ayend...@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.
