Hi Vincent:
- Field inhomogeneity correction: This is done using the FSL fugue utility, which uses a field map to mitigate the geometric distortions in the DWI due to field inhomogeneity. However, as you point out, DWI-to-T1 registration will be performed anyway, and this may mitigate this type of geometric distortions.
- Number of sticks: How many you can fit to your data depends on the angular resolution in your data. You can keep adding parameters to the model, but if there's not enough data to estimate those parameters reliably, there's no point. You can get an idea from Behrens et al 2007 on what's feasible.
- The one MCMC parameter that may be useful to play with is nsample, the total number of path samples collected. Particularly for longitudinal, you may want to increase it if the tracts look narrow, since it may take longer to sample the full tract with data from more than one time point.
Hope this helps, a.y
On Wed, 17 Apr 2013, vbrunsch@nmr.mgh.harvard.edu wrote:
Hi all! I am almost ready to do my first longitudinal run with Tracula. I guess that for the remaining insecurities it is probably best to stick with the default options but I'd like to be more confident with it and just wanted to ask which option to choose and why or why not:
My config file contains information about two time points of 39 subjects.
- Perform "Registration-based B0-inhomogeneity compensation"
If I understand correctly, although I would have the fieldmap information this step (as well as BET) is not necessary as I can use the respective T1 weighted image (usemaskanat=1) for registration?
- Number of sticks in the ball-stick model
Since last month it is possible to change the default value of 2. Would you recommend a higher value? That would give me more information also about crossing fibers, right? But if so, which value would be reasonable and why?
- MCMC burn-in iterations (default:200), iterations (default:7500) and
frequency (default:5) (Why are we allowed to change these options at all?)
Thank you! Best, Vincent _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer