Hi Joëlle - I highly recommend using the TRACULA version in 6.0, because it tries to detect the cases that need to be reinitialized and reruns them automatically. (It's ok if the anatomical segmentations come from the 5.3 version of recon-all.) Of course, like with any automatic method for detecting outliers, it relies on some threshold for calling something an outlier, so there may always a few cases that need to be rerun that just fall on the wrong side of that threshold. So visual inspection is always recommended.
In 6.0, TRACULA uses the new mri_convert to extract the gradient table and b-value table. These and other changes are listed in the release notes: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Best, a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van Der Molen [Joelle.Vandermolen@etu.unige.ch] Sent: Wednesday, March 08, 2017 8:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA tract reconstruction
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