Dwipreproc: What's the difference between -rpe_pair and -rpe_all? Which one should be used for HCP data?

Hi Liyuan,

The HCP tutorial was written purely for users to be able to recreate the analysis pipeline that was demonstrated at ISMRM in 2015. So it shouldn’t be interpreted as the “recommended” pipeline for using HCP data, and probably won’t be kept up-to-date with new and future developments.

With regards to B1 bias field specifically, the bias field is in fact quite strong in HCP data and so in general I would in fact recommend using it. Without it, SIFT will still be beneficial; but the strength of the bias present in the B1 field will propagate through to the resulting connection densities.

We additionally have a novel method that performs both bias field correction and intensity normalisation in a single step. It was included in yesterday’s release candidate update as the command mtbin (whoops, it didn’t get included in the list of new executables! Fixed.), and is listed in the instructions for fixel-based analysis of multi-shell data. For anyone here at ISMRM, this method will be presented today at 2:45 at computer 95 (abstract 3541) (look for @Thijs).

Cheers
Rob