Create check_tr.py

Extracts TR information in header of functional (MNI space) image and checks if it matches TR provided in config file. If they are different, updates the TR from one of two sources and passes a warning.
Deleted check_tr.py
Update registration.py

Temporarily removed warp resolution parameters to see effect on registration quality
Update cpac_pipeline.py

Introduced path to config file parameter "configFileTwomm" to fnirt input 'fnirt_config' (reg_anat_mni)
Update __init__.py

Incremented version of 'development' branch to 0.3.1 to reflect changes to registration workflow.
Merge branch 'development' of https://github.com/FCP-INDI/C-PAC
Update config.yml

Added fnirtWarpResolution parameter for the option of a user-specified FNIRT configuration
Added support for user-specified FNIRT parameter warp_resolution via the pipeline config file.
Merge branch 'development' of https://github.com/FCP-INDI/C-PAC
Update registration.py

Removed hard-coded warp resolution input parameter.
Update cpac_pipeline.py

Fixed the fnirt_config input parameter to pass the correct value (as per updated config.yml file).

fnirt_config input of reg_anat_mni only accepts the name of the FSL config file, not the entire path. As per the Nipype documentation:

FSL FNIRT > Inputs > Optional

"config_file: ('T1_2_MNI152_2mm' or 'FA_2_FMRIB58_1mm' or an existing file name)
        Name of config file specifying command line arguments"
Update anatomical.py

Added the FSL FNIRT configuration file editing option.
Update registration.py

Temporarily including hard-coded input parameters for FNIRT, including default recommended parameters.
Update __init__.py

Updated version number.
Update __init__.py

Wait until full functionality of FNIRT warp res override in GUI to move up to 0.3.2.
Merge branch 'development' of https://github.com/FCP-INDI/C-PAC

Conflicts:
	CPAC/pipeline/cpac_pipeline.py
	CPAC/registration/registration.py
Merge branch 'master' of https://github.com/sgiavasis/C-PAC
Fixed conflicts.
Returned FSL config file as input parameter, but did not remove hard-coded inputs yet.
Update config.yml

Allowed temporary switching of custom FNIRT inputs.