add ExtractMainComponent interface
Merge branch 'master' into enh/freesurfer

* master: (255 commits)
  fix: version property
  doc: added pointer to ants example
  fix: removed cma to freesurfer mapping, updated docs and pointed to atlas/template downloads
  fix: remove np deprecation decorator and moved imports to run_interface.
  fix: explicitly test for nipy version and remove imports to specific interfaces closes #648
  Added FuzzyOverlap to changelog
  fix: set slice_times as seconds outside workflow generating function
  fix: replaced plugin_args with proper arguments
  enh: replace realignment routine with newer Nipype interface for Nipy's newer class
  enh: added SpaceTimeRealign from nipy 0.4.dev
  api: always run datasink and let copyfiles decide if things need to be copied or not. in case inputs are directories, this will allow refreshing outputs.
  fix: moved imports for dicominfo outside of the function
  fix: use ceiling of slice thickness for erosion purposes
  fix: add imports to the functions
  enh: compressing more into functions
  enh: replaced erosion with slicethickness and added epimask support for bbregister
  fix: updated ants example to use new parameters from ants
  tst: fixed ants doctests to indicate smoothing sigmas
  enh: updated antsApplyTransforms to accept input image type
  api: changed smoothing sigmas to accept float in antsRegistration
  ...
Merge branch 'master' into enh/freesurfer

* master:
  fix: afni url in afni package
  added more documentation
  Added dummy files
  fixed inputs for Retroicor
  adding retrocicor to __init__.py
  addition of 3dretroicor interface, very basic version
  enh: allow naming a workflow
  microseconds
  microseconds
  fix:total_seconds_python2.6
  fix: missing template
  enh: updated mindboggle atlases
  DOC: Add short doc page for SelectFiles
allow freesurfer resume... test
allow freesurfer resume, wip
fix logging
fix logging
fix logging
fix freesurfer steps  resume
Merge branch 'master' into enh/freesurfer

* master:
  add DicomImport to spm init.py
  fix merge conflict in CHANGES
  add interface for spm's dicom import
  spm wants a two-item array here
  Fence matplotlib import with try block
  Get backend configurable from node config
  Set matplotlib backend from config in pyscript
  Attempt to set backend in local matplotlib
  fix: matplotlib import to inside function
  added changelog information
  enh: update internal prov to latest version of external library
  added hash_file protocol and dummy test file
  Remove inheritance_diagram.py.
  now able to set prefix and file extension automatically NIFTI
  include AFNItoNIFTI in module init file
  include 3dAFNItoNIFTI command in interfaces.afni
Merge branch 'master' into enh/freesurfer

* master: (178 commits)
  fix: ridiculous mistakes
  fix: make sure mandatory=False items are displayed
  fix: mesh import to enable doc building
  doctest fixes
  docs and changelog
  changelog
  Fixed tests
  enh: added options to execute script from command line
  fix: fix env again
  fix: proper environment access
  fix: tests and added new data files
  fix: updated checking script
  fix: updating fsl metadata
  fix: updated all inappropriate metadata  (fsl update in separate commit)
  Added nocheck option in fielmap_correction
  enh: added script to check metadata
  Fixed cmdline commands in docstrings
  Revert "Run autopep8 on misc.py"
  Fixed failed test
  Fixed errors in Doctest (?)
  ...
doctest fix
Merge remote branch 'nipype/master' into enh/freesurfer

* nipype/master:
  Removed left over class
  PEP8
  fixed import
  backward compatibility import
  added mandatory dtatgrabber field
  removed doubled declaration
  fixed a typo
  backward compatibility import
  fix: more dict comprehension fixes
  fix: ordered dict
  fix: change dict comprehension to list comprehension for 2.6 compatibility
  doc: updated CHANGES to reflect new name generation mechanism
  enh: updated FLIRT to use new name generation mechanism to match with doc example
  doc: added information about new name generation mechanism
  Additionnal correction to FSL invwarp. Missing option from Camino dtifit
  fsl/utils.py: fix error from InvWarp generated filename
  fix: removed all mandatory=False
  fix: make sure mandatory=False items are displayed
  fix: added name_template to metadata keys
  ref: changing filename generation to a more consistent model
resume overwrite cmdline
minor fixes, ExtractMainComponent still have test failure for extension problems (.pial)
fix: allow for template specification in at the input level
spm rewrites headers on these files

in some workflows, you want to use the files with the modified headers,
not resliced images. So we'll just return the in_files in the output.
See SPM doco Chapter 2: Realign FMI:
http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf
enable list of list of files from slice time output

looks like the variable 'run' never gets used… perhaps a typo.

output spec needed adjustment to handle list of lists.
fix indents - nothing real
normalize can take a list of lists of files as input.