??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