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
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
stdp82＠virgilio.it