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nipype.interfaces.io
====================


:class:`DataGrabber`
--------------------


Generic datagrabber module that wraps around glob in an
intelligent way for neuroimaging tasks to grab files


.. note::
   Doesn't support directories currently

Examples
~~~~~~~~

>>> from nipype.interfaces.io import DataGrabber

Pick all files from current directory

>>> dg = DataGrabber()
>>> dg.inputs.template = '*'

Pick file foo/foo.nii from current directory

>>> dg.inputs.template = '%s/%s.dcm'
>>> dg.inputs.template_args['outfiles']=[['dicomdir','123456-1-1.dcm']]

Same thing but with dynamically created fields

>>> dg = DataGrabber(infields=['arg1','arg2'])
>>> dg.inputs.template = '%s/%s.nii'
>>> dg.inputs.arg1 = 'foo'
>>> dg.inputs.arg2 = 'foo'

however this latter form can be used with iterables and iterfield in a
pipeline.

Dynamically created, user-defined input and output fields

>>> dg = DataGrabber(infields=['sid'], outfields=['func','struct','ref'])
>>> dg.inputs.base_directory = '.'
>>> dg.inputs.template = '%s/%s.nii'
>>> dg.inputs.template_args['func'] = [['sid',['f3','f5']]]
>>> dg.inputs.template_args['struct'] = [['sid',['struct']]]
>>> dg.inputs.template_args['ref'] = [['sid','ref']]
>>> dg.inputs.sid = 's1'

Change the template only for output field struct. The rest use the
general template

>>> dg.inputs.field_template = dict(struct='%s/struct.nii')
>>> dg.inputs.template_args['struct'] = [['sid']]

Inputs:: 

	[Mandatory]
	template : (a string)
		Layout used to get files. relative to base directory if defined

	[Optional]
	base_directory : (an existing directory name)
		Path to the base directory consisting of subject data.
	field_template : (a dictionary with keys which are 'outfiles' and with values which are any value)
		arguments that fit into template
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	raise_on_empty : (a boolean)
		Generate exception if list is empty for a given field
	sort_filelist : (a boolean)
		Sort the filelist that matches the template
	template_args : (a dictionary with keys which are a string and with values which are a list of items which are a list of items which are any value)
		Information to plug into template


Outputs:: 

	outfiles	Unknown

:class:`DataSink`
-----------------


Generic datasink module to store structured outputs

Primarily for use within a workflow. This interface allows arbitrary
creation of input attributes. The names of these attributes define the
directory structure to create for storage of the files or directories.

The attributes take the following form:

string[[.[@]]string[[.[@]]string]] ...

where parts between [] are optional.

An attribute such as contrasts.@con will create a 'contrasts' directory to
store the results linked to the attribute. If the @ is left out, such as in
'contrasts.con', a subdirectory 'con' will be created under 'contrasts'.

Notes
~~~~~

    Unlike most nipype-nodes this is not a thread-safe node because it can
    write to a common shared location. It will not complain when it
    overwrites a file.

Examples
~~~~~~~~

>>> ds = DataSink()
>>> ds.inputs.base_directory = 'results_dir'
>>> ds.inputs.container = 'subject'
>>> ds.inputs.structural = 'structural.nii'
>>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii'])
>>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii'])
>>> ds.run() # doctest: +SKIP

Inputs:: 

	[Optional]
	_outputs : (a dictionary with keys which are a string and with values which are any value)
		Unknown
	base_directory : (a directory name)
		Path to the base directory for storing data.
	container : (a string)
		Folder within base directory in which to store output
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	parameterization : (a boolean)
		store output in parametrized structure
	regexp_substitutions : (a tuple of the form: (a string, a string))
		List of 2-tuples reflecting a pair of a Python regexp pattern and a replacement string. Invoked after string `substitutions`
	remove_dest_dir : (a boolean)
		remove dest directory when copying dirs
	strip_dir : (a directory name)
		path to strip out of filename
	substitutions : (a tuple of the form: (a string, a string))
		List of 2-tuples reflecting string to substitute and string to replace it with



:class:`FreeSurferSource`
-------------------------


Generates freesurfer subject info from their directories

Examples
~~~~~~~~

>>> from nipype.interfaces.io import FreeSurferSource
>>> fs = FreeSurferSource()
>>> #fs.inputs.subjects_dir = '.'
>>> fs.inputs.subject_id = 'PWS04'
>>> res = fs.run() # doctest: +SKIP

>>> fs.inputs.hemi = 'lh'
>>> res = fs.run() # doctest: +SKIP

Inputs:: 

	[Mandatory]
	subject_id : (a string)
		Subject name for whom to retrieve data
	subjects_dir : (a directory name)
		Freesurfer subjects directory.

	[Optional]
	hemi : ('both' or 'lh' or 'rh')
		Selects hemisphere specific outputs
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run


Outputs:: 

	T1 : (an existing file name)
		Intensity normalized whole-head volume
	annot : (an existing file name)
		Surface annotation files
	aparc_aseg : (an existing file name)
		Aparc parcellation projected into aseg volume
	aseg : (an existing file name)
		Volumetric map of regions from automatic segmentation
	brain : (an existing file name)
		Intensity normalized brain-only volume
	brainmask : (an existing file name)
		Skull-stripped (brain-only) volume
	curv : (an existing file name)
		Maps of surface curvature
	filled : (an existing file name)
		Subcortical mass volume
	inflated : (an existing file name)
		Inflated surface meshes
	label : (an existing file name)
		Volume and surface label files
	norm : (an existing file name)
		Normalized skull-stripped volume
	nu : (an existing file name)
		Non-uniformity corrected whole-head volume
	orig : (an existing file name)
		Base image conformed to Freesurfer space
	pial : (an existing file name)
		Gray matter/pia mater surface meshes
	rawavg : (an existing file name)
		Volume formed by averaging input images
	ribbon : (an existing file name)
		Volumetric maps of cortical ribbons
	smoothwm : (an existing file name)
		Smoothed original surface meshes
	sphere : (an existing file name)
		Spherical surface meshes
	sphere_reg : (an existing file name)
		Spherical registration file
	sulc : (an existing file name)
		Surface maps of sulcal depth
	thickness : (an existing file name)
		Surface maps of cortical thickness
	volume : (an existing file name)
		Surface maps of cortical volume
	white : (an existing file name)
		White/gray matter surface meshes
	wm : (an existing file name)
		Segmented white-matter volume
	wmparc : (an existing file name)
		Aparc parcellation projected into subcortical white matter

:class:`IOBase`
---------------




Inputs:: 

	[Optional]
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run



:class:`SQLiteSink`
-------------------


:class:`XNATSink`
-----------------


Generic datasink module that takes a directory containing a
list of nifti files and provides a set of structured output
fields.

Inputs:: 

	[Mandatory]
	config : (a file name)
		Unknown
		exclusive: server
	experiment_id : (a string)
		Set to workflow name
	project_id : (a string)
		Project in which to store the outputs
	server : (a string)
		Unknown
		exclusive: config
		requires: user,pwd
	subject_id : (a string)
		Set to subject id

	[Optional]
	_outputs : (a dictionary with keys which are a string and with values which are any value)
		Unknown
	assessor_id : (a string)
		Option to customize ouputs representation in XNAT - assessor level will be used with specified id
		exclusive: reconstruction_id
	cache_dir : (a directory name)
		
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	pwd : (a string)
		Unknown
	reconstruction_id : (a string)
		Option to customize ouputs representation in XNAT - reconstruction level will be used with specified id
		exclusive: assessor_id
	share : (a boolean)
		Option to share the subjects from the original projectinstead of creating new ones when possible - the created experiments are then shared backk to the original project
	user : (a string)
		Unknown



:class:`XNATSource`
-------------------


Generic XNATSource module that wraps around the pyxnat module in
an intelligent way for neuroimaging tasks to grab files and data
from an XNAT server.

Examples
~~~~~~~~

>>> from nipype.interfaces.io import XNATSource

Pick all files from current directory

>>> dg = XNATSource()
>>> dg.inputs.template = '*'

>>> dg = XNATSource(infields=['project','subject','experiment','assessor','inout'])
>>> dg.inputs.query_template = '/projects/%s/subjects/%s/experiments/%s'                    '/assessors/%s/%s_resources/files'
>>> dg.inputs.project = 'IMAGEN'
>>> dg.inputs.subject = 'IMAGEN_000000001274'
>>> dg.inputs.experiment = '*SessionA*'
>>> dg.inputs.assessor = '*ADNI_MPRAGE_nii'
>>> dg.inputs.inout = 'out'

>>> dg = XNATSource(infields=['sid'],outfields=['struct','func'])
>>> dg.inputs.query_template = '/projects/IMAGEN/subjects/%s/experiments/*SessionA*'                    '/assessors/*%s_nii/out_resources/files'
>>> dg.inputs.query_template_args['struct'] = [['sid','ADNI_MPRAGE']]
>>> dg.inputs.query_template_args['func'] = [['sid','EPI_faces']]
>>> dg.inputs.sid = 'IMAGEN_000000001274'

Inputs:: 

	[Mandatory]
	config : (a file name)
		Unknown
		exclusive: server
	query_template : (a string)
		Layout used to get files. Relative to base directory if defined
	server : (a string)
		Unknown
		exclusive: config
		requires: user,pwd

	[Optional]
	cache_dir : (a directory name)
		Cache directory
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	pwd : (a string)
		Unknown
	query_template_args : (a dictionary with keys which are a string and with values which are a list of items which are a list of items which are any value)
		Information to plug into template
	user : (a string)
		Unknown


Outputs:: 

	outfiles	Unknown
