.. AUTO-GENERATED FILE -- DO NOT EDIT!

nipype.algorithms.misc
======================


:class:`CreateNifti`
--------------------




Inputs:: 

	[Mandatory]
	data_file : (an existing file name)
		ANALYZE img file
	header_file : (an existing file name)
		corresponding ANALYZE hdr file

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


Outputs:: 

	nifti_file : (an existing file name)
		Unknown

:class:`Distance`
-----------------


Calculates distance between two volumes.

Inputs:: 

	[Mandatory]
	volume1 : (an existing file name)
		Has to have the same dimensions as volume2.
	volume2 : (an existing file name)
		Has to have the same dimensions as volume1.

	[Optional]
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	method : ('eucl_min' or 'eucl_cog' or 'eucl_mean' or 'eucl_wmean')
		""eucl_min": Euclidean distance between two closest points    "eucl_cog": mean Euclidian distance between the Center of Gravity of volume1 and CoGs of volume2    "eucl_mean": mean Euclidian minimum distance of all volume2 voxels to volume1    "eucl_wmean": mean Euclidian minimum distance of all volume2 voxels to volume1 weighted by their values


Outputs:: 

	distance : (a float)
		Unknown
	histogram : (a file name)
		Unknown
	point1 : (an array with shape (3,))
		Unknown
	point2 : (an array with shape (3,))
		Unknown

:class:`ModifyAffine`
---------------------


Left multiplies the affine matrix with a specified values. Saves the volume as a nifti file.

Inputs:: 

	[Mandatory]
	volumes : (an existing file name)
		volumes which affine matrices will be modified

	[Optional]
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	transformation_matrix : (an array with shape (4, 4))
		transformation matrix that will be left multiplied by the affine matrix


Outputs:: 

	transformed_volumes : (a file name)
		Unknown

:class:`Overlap`
----------------


Calculates various overlap measures between two maps.

Example
~~~~~~~

>>> overlap = Overlap()
>>> overlap.inputs.volume1 = 'cont1.nii'
>>> overlap.inputs.volume1 = 'cont2.nii'
>>> res = overlap.run() # doctest: +SKIP

Inputs:: 

	[Mandatory]
	volume1 : (an existing file name)
		Has to have the same dimensions as volume2.
	volume2 : (an existing file name)
		Has to have the same dimensions as volume1.

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


Outputs:: 

	dice : (a float)
		Unknown
	diff_file : (an existing file name)
		Unknown
	jaccard : (a float)
		Unknown
	volume_difference : (an integer)
		Unknown

:class:`PickAtlas`
------------------


Returns ROI masks given an atlas and a list of labels. Supports dilation
and left right masking (assuming the atlas is properly aligned).

Inputs:: 

	[Mandatory]
	atlas : (an existing file name)
		Location of the atlas that will be used.

	[Optional]
	dilation_size : (an integer)
		Defines how much the mask will be dilated (expanded in 3D).
	hemi : ('both' or 'left' or 'right')
		Restrict the mask to only one hemisphere: left or right
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	labels : (an integer or a list of items which are an integer)
		Labels of regions that will be included in the mask. Must be compatible with the atlas used.
	output_file : (a file name)
		Where to store the output mask.


Outputs:: 

	mask_file : (an existing file name)
		output mask file

:class:`SimpleThreshold`
------------------------




Inputs:: 

	[Mandatory]
	threshold : (a float)
		volumes to be thresholdedeverything below this value will be set to zero
	volumes : (an existing file name)
		volumes to be thresholded

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


Outputs:: 

	thresholded_volumes : (an existing file name)
		thresholded volumes

:class:`TSNR`
-------------


Computes the time-course SNR for a time series

Typically you want to run this on a realigned time-series.

Example
~~~~~~~

>>> tsnr = TSNR()
>>> tsnr.inputs.in_file = 'functional.nii'
>>> res = tsnr.run() # doctest: +SKIP

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		realigned 4D file

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


Outputs:: 

	tsnr_file : (an existing file name)
		tsnr image file
