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 > > > >
dmrirc_single_subject4d
Description: Binary data
_______________________________________________ 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.
