api: force users to explicitly define whether to sort files
New EPI dewarping using a workflow

This new feature implements the EPI dewarping methodology from epidewarp.fsl,
as a workflow and including some enhancements allowing:
  * Use for dMRI
  * Optional registration
  * New EPI parameters support (parallel imaging, reverse encoding)

Additionally, some improvements on the FSL FUGUE's API have been included:
  * Added --saveshift argument support
  * Added --warp argument support
  * Improved the output listing methods for coherence
New EPI dewarp workflow (#525)

  * Removed useless comment
  * Changelog updated
First implementation for MBIS
Standardized import to add all utilities at once
Added MBIS to sub-package configuration list
Minor fixes

  * Added pipeline to __init__.py so its loadable the same way the others are
  * Polished code in pipeline creation
Update legacy.py - buildtemplateparallel.sh

The value of 'j' has to be changed into a string, otherwise you'll end up with "TypeError: cannot concatenate 'str' and 'int' objects" and the command can't be passed on to the console.
buildtemplateparallel.sh - issue with input files

If I have an array of inputs like: 

in_files = ['~/data/subject_1/struct.nii','~/data/subject_2/struct.nii','~/data/subject_3/struct.nii']

The current code would turn this into the command:

buildtemplateparallel.sh -d 3 -n 1 -g 0.250000 -i 3 -m 30x90x20 -j 4 -o PREFIX -c 2 -r 1 -s PR -t GR struct.nii struct.nii struct.nii

Like this, I'm not able to run the buildtemplateparallel interface with Nipype. I think it crashes because it can't find the files. My commit changes the command to the following:

buildtemplateparallel.sh -d 3 -n 1 -g 0.250000 -i 3 -m 30x90x20 -j 4 -o PREFIX -c 2 -r 1 -s PR -t GR ~/data/subject_1/struct.nii ~/data/subject_2/struct.nii ~/data/subject_3/struct.nii

Like this the full path to structural images is passed to the command and it works.
Merge pull request #525 from oesteban/master

New EPI dewarping workflow, in a similar manner to eddy_current correction
Merge pull request #526 from miykael/patch-1

Update legacy.py - buildtemplateparallel.sh
Polished code

Removed some useless functions and improved susceptibility pipeline
Modified FSL FLIRT interface to provide log support

In order that supporting logging for fdt_rotate_bvecs script,
the verbose output of FLIRT is saved to file if the save_log input
is provided.
Added motion correction pipeline

  * Added motion correction pipeline, rotating the b-matrix
  * Some minor fixes on the rest of pipelines
Updated dMRI and fMRI pre-processing

  * ENH: modified parameter for parallel imaging, now it is possible to modify the acceleration factor
  * ENH: created new pipeline for full dMRI-EPI full distortions correction. Includes: motion, eddy currents and susceptibility correction
Updated changelog
Removed accidentally added files (#530)

Removed files regarding MBIS tool
Fixed some details for the PR #530

  * Improved documentation, and added warning about bvec rotation
  * Improved FSL FLIRT interface to support spline interpolation
  * Added spline interpolation wherever resampling is required
  * Syntax checked with autopep8
Merge pull request #530 from oesteban/enh/dMRIPreprocessing

dMRI pre-processing (complete)
Merge pull request #527 from miykael/patch-2

buildtemplateparallel.sh - issue with input files