fixing wrong output directory in afni base gen_filename
Merge branch 'master' into bug/afni

* master:
  changelog
  DOctest fix
  PEP8
  add doc
  DOC: Update info on Condor and its plugins.
  DOC: Fix documentation glitch
  BF: Use unique filenames for DAGMan workflows
  enh: remove logger dump added in 9d6b1a86921982b84f17b75ebf1a515f1d8710f7
  fix in NewSegment warp field output options
  fix: ensure that commandline calls force terminal output if stdout or stderr is required
  fix: failing flirt test
  fix: doctest for commandline
  doc: added change note
  enh: allow commandline interfaces to control terminal output
  adding trim interface that keeps the original dtype storage
Fixing Resample inheritance
Allow out_file to be alternatively not generated
Merge branch 'master' into bug/afni

* master:
  added maths.MaxImage examples
  test maths.MaxImage for fslmaths -Tmax option
  add maths.MaxImage for fslmaths -Tmax option
  fix: change type of loops,speedup and between loops so its compatible with changes in the nipy code
fixing Automask
abspath for Automask
fix: when using mcr set nodesktop and nosplash to undefined
fixes
BF: Don't fail when CopyMeta gets a Nifti without meta data
Just create an empty extension.
fixed output collection for antsRegistration
added mask input for bias field correction
BF: Fix SplitNifti to generate unique filenames for outputs.
Merge pull request #521 from chrisfilo/fix/ants_outputs

Fix/ants outputs
Merge pull request #524 from moloney/bf-split-nifti

BF: Fix SplitNifti to generate unique filenames for outputs.
Merge pull request #518 from moloney/bf-copy-meta-nullop

BF: Don't fail when CopyMeta gets a Nifti without meta data
Merge pull request #516 from satra/fix/mcr

WIP: when using mcr set nodesktop and nosplash to undefined
Merge pull request #504 from bpinsard/bug/afni

fixing wrong output directory in afni base gen_filename
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