Dear Joelle,
regarding the conversion to .bvecs, could you please show the example of difference between bvecs converted by mri_convert of FreeSurfer and mrconvert of mrtrix3?
Do you have most recent version of mrtrix3? There have been a quite extensive discussion on implementation of FSL .bvec convention in mrtrix3 in spring 2016:
http://www.mrtrix.org/2016/04/15/bug-in-fsl-bvecs-handling/
However, there have been quite a big effort to settle this issue and I am pretty convinced that the recent versions should have this issue resolved.
Maybe you can also post this to the mrtrix community forum, they are usually responding very quickly and each post gives detailed attention.
Regards,
Antonin Skoch
??Dear Tracula experts,
I am applying Tracula on a longitudinal data set, and have some questions I am
hoping you could help me with:
Firstly, upon visual inspection, several tracts appear to be quite messy, or
small (on the default freeview threshold) for most subjects. However, the -stat
step from Tracula does not necessarily flag these tracts as outliers. What is
then the best way to decide whether tracts are not correctly reconstructed and
need to be rerun separately once more? Can I rely on the flagged outliers? Or
should I rerun all the tracts that do not look ok after visual inspection? And
in the last case, for tracts that look small, are they considered as correctly
reconstructed if looking ok at lower thresholds than the default of freeview?
Second, concerning the rerunning of poorly reconstructed tracts, I was
wondering if there might be a more automated way to configure the dmrirc file
in order to adapt it for each subject/each tract to rerun (and its
corresponding control points).
Third, I was wondering if there is a recommended software for obtaining bvecs
and bvals. For the moment I used mrconvert (from MRtrix, using the
-export_grad_fsl option) and the new mri_convert from freesurfer 6.0. As they
give different outputs, I was wondering if this may impact the reconstruction.
Lastly, would you recommend using freesurfer 5.3 or 6.0 for applying the
longitudinal stream of Tracula? Related to this, is it recommended to use the
same freesurfer version to obtain the long/base images, and to run Tracula?
Thank you for your time,
Best regards,
Joëlle van der Molen