simple crop interfaces that keeps oblique matrices
add Trim and Crop to __init__.py
allow None in Crop as default
output in same type as input
create a nipy base interface for filetype handling etc... did not updated all the existing interfaces though
add padding option to crop
Merge branch 'master' into nipy/trim

* master:
  added maths.MaxImage examples
  test maths.MaxImage for fslmaths -Tmax option
  add maths.MaxImage for fslmaths -Tmax option
Merge branch 'master' into nipy/trim

* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR #530
  Removed accidentally added files (#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
Merge branch 'master' into nipy/trim

* master: (54 commits)
  constrain write_which to length 2
  BF: Fix issue where unicode paths were not recognized as files.
  changelog
  Doctests fix
  Fixed tests.
  in fact masking wasn't working, HistogramRegistration takes mask as numpy not nibabel
  allow similarity computation without mask
  Added [xor] metadata to afni.AutoTcorrelate
  added mask_source option to afni.AutoTcorrelate
  added mask_source option to afni.AutoTcorrelate
  Fixed error in _rotate_bvec that was adding an extra entry to the output rotated_bvecs file and offsetting the correction by one volume.
  fix fugue for not necessarly wanted output
  add Bandpass to init
  homogenize name function accross interfaces
  fixing for new gen_filename autopep8
  autopep8
  few interfaces added, pep8
  add min version for bbr options
  pep8
  doctest
  ...
fix Trim interface
default_output_type
squeeze last dim if len 1
Merge branch 'master' into nipy/trim

* master: (110 commits)
  back to dev
  Fixed links to old docs.
  0.8 release
  fix: check if output directory exists before determining results file location. needs better reporting of the error.
  fix: fixed node configuration errors
  fix: clean up spm example
  doc: added to changes
  enh: allow node specific configuration to override master config
  doc: spelling
  Fixed a typo and added Hans grants.
  fixed a typo added INCF
  daniel-ge + double list
  New upgraded about page.
  doc: clarify nipy slice timing
  enh: updated smri ants example to use suggested defaults from the ants dev team
  Does not crash if SPM is not installed.
  make some ANTS inputs mandatory
  Added missing unit inputs.
  fix: tests, absolute path on outputs
  fix: output image names
  ...
fix the outputtype
fix outputtype
Merge branch 'master' into nipy/trim

* master: (23 commits)
  fix: added svg neurodebian logo
  fix: notebook links to latest version
  enh: updated tutorial
  fix: broken test to reflect interface changes.
  Slight correction to previous PR
  Fix SPM interfaces
  fix: mark's last name
  fix: updated tutorial to include download of data
  enh: added tutorial notebook
  fix: reverted fix while keeping changed meta tag.
  each time I use an afni interface I have not been using for a long time I spend 4 hours fixing some bugs that goes down to base interface specs......
  fix tcorrmap for use of source_name, depends on recent fix cline_bug branch
  where does source_name come from? should fix a lot of gen_file in afni other than out_file
  fixe name_source traits
  fix the TCorrMap histogram options
  doc: update information on output options for CommandLine interfaces
  tst: added doctest ellipses to fix afni tests
  tst: added missing doctest file maps.nii
  fix: changed input name for 3dallineate
  fix: clean up fsl model tests.
  ...
Merge branch 'master' into nipy/trim

* master: (64 commits)
  PEP8
  Added human order sorting for FLAMEO outputs, fixed abspath for Cluster outputs.
  added back the fstat outputs to fsl flameo interface
  enh: replace id extraction with regular expression
  fix: check only the last line in the sge qsub stdout
  FIX broken MapNode doctest
  Added XOR condition between apply_isoxfm and apply_xfm
  fix imports
  Solve Merge issue
  Solve merge issue
  PEP8
  Add missing option apply_isoxfm to FSL Flirt wrapper
  Merge and clean up FSLGLM into GLM.
  added FSLGLM
  doc: fixed building with Sphinx 1.2
  Updating CHANGES
  base_dir in Workflow
  Updating pipeline docstrings
  Reversing the order of the name and iterfield args in MapNode
  Also making iterfield positional in MapNode
  ...
fixing doc test
merge
Merge branch 'master' into nipy/trim

* 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