nipy/nipype — pull request #530 by oesteban (2013-03-06 14:02:37+00:00)
Title: dMRI pre-processing (complete)

Continuing with #525, a full pre-processing pipeline for dMRI is proposed:
* Motion correction artifact: a new workflow is created with rigid registration (6 degrees of freedom) among volumes, and rotation of the B-matrix (Leemans et al. 2007 - http://www.ncbi.nlm.nih.gov/pubmed/19319973).
* Eddy currents correction: some minor improvements (explicitly set affine registration), following (Rolheiser 2011 [online: http://wiredminds.blogspot.com.es/2011/06/dti-preprocessing-in-fsl-b-vector.html]).
* Epidewarp.fsl script has been renamed to 'susceptibility' correction and added some extra features (the most important one being the possibility to introduce the GRAPPA acceleration factor if parallel imaging was used).
* A new workflow integrating the 3 elements for dMRI correction.

TODO: it would be nice to separate workflows for consistency, collecting all of them simultaneously appropriate for fMRI and dMRI on one side and separating the ones specific for dMRI (the motion correction pipeline and the full pre-processing pipeline).