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nipype.interfaces.diffusion_toolkit.dti
=======================================


:class:`DTIRecon`
-----------------


Wraps command **dti_recon**

Use dti_recon to generate tensors and other maps

Inputs:: 

	[Mandatory]
	DWI : (an existing file name)
		Input diffusion volume
	bvals : (an existing file name)
		b values file
	bvecs : (an existing file name)
		b vectors file

	[Optional]
	args : (a string)
		Additional parameters to the command
	b0_threshold : (a float)
		program will use b0 image with the given threshold to mask out high
        background of fa/adc maps. by default it will calculate threshold
        automatically. but if it failed, you need to set it manually.
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	image_orientation_vectors : (a list of from 6 to 6 items which are a float)
		specify image orientation vectors. if just one argument given,
        will treat it as filename and read the orientation vectors from
        the file. if 6 arguments are given, will treat them as 6 float
        numbers and construct the 1st and 2nd vector and calculate the 3rd
        one automatically.
        this information will be used to determine image orientation,
        as well as to adjust gradient vectors with oblique angle when
	n_averages : (an integer)
		Number of averages
	oblique_correction : (a boolean)
		when oblique angle(s) applied, some SIEMENS dti protocols do not
        adjust gradient accordingly, thus it requires adjustment for correct
        diffusion tensor calculation
	out_prefix : (a string)
		Output file prefix
	output_type : ('nii' or 'analyze' or 'ni1' or 'nii.gz')
		output file type


Outputs:: 

	ADC : (an existing file name)
		Unknown
	B0 : (an existing file name)
		Unknown
	FA : (an existing file name)
		Unknown
	FA_color : (an existing file name)
		Unknown
	L1 : (an existing file name)
		Unknown
	L2 : (an existing file name)
		Unknown
	L3 : (an existing file name)
		Unknown
	V1 : (an existing file name)
		Unknown
	V2 : (an existing file name)
		Unknown
	V3 : (an existing file name)
		Unknown
	exp : (an existing file name)
		Unknown
	tensor : (an existing file name)
		Unknown

:class:`DTITracker`
-------------------


Wraps command **dti_tracker**



Inputs:: 

	[Mandatory]
	mask1_file : (a file name)
		first mask image

	[Optional]
	angle_threshold : (a float)
		set angle threshold. default value is 35 degree
	angle_threshold_weight : (a float)
		set angle threshold weighting factor. weighting will be be applied         on top of the angle_threshold
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	input_data_prefix : (a string)
		for internal naming use only
	input_type : ('nii' or 'analyze' or 'ni1' or 'nii.gz')
		input and output file type. accepted values are:
        analyze -> analyze format 7.5
        ni1     -> nifti format saved in seperate .hdr and .img file
        nii     -> nifti format with one .nii file
        nii.gz  -> nifti format with compression
        default type is 'nii'
	invert_x : (a boolean)
		invert x component of the vector
	invert_y : (a boolean)
		invert y component of the vector
	invert_z : (a boolean)
		invert z component of the vector
	mask1_threshold : (a float)
		threshold value for the first mask image, if not given, the program will         try automatically find the threshold
	mask2_file : (a file name)
		second mask image
	mask2_threshold : (a float)
		threshold value for the second mask image, if not given, the program will         try automatically find the threshold
	output_file : (a file name)
		Unknown
	output_mask : (a file name)
		output a binary mask file in analyze format
	primary_vector : ('v2' or 'v3')
		which vector to use for fibre tracking: v2 or v3. If not set use v1
	random_seed : (an integer)
		use random location in a voxel instead of the center of the voxel           to seed. can also define number of seed per voxel. default is 1
	step_length : (a float)
		set step length, in the unit of minimum voxel size.
        default value is 0.5 for interpolated streamline method
        and 0.1 for other methods
	swap_xy : (a boolean)
		swap x & y vectors while tracking
	swap_yz : (a boolean)
		swap y & z vectors while tracking
	swap_zx : (a boolean)
		swap x & z vectors while tracking
	tensor_file : (an existing file name)
		reconstructed tensor file
	tracking_method : ('fact' or 'rk2' or 'tl' or 'sl')
		fact -> use FACT method for tracking. this is the default method.
        rk2  -> use 2nd order runge-kutta method for tracking.
        tl   -> use tensorline method for tracking.
        sl   -> use interpolated streamline method with fixed step-length


Outputs:: 

	mask_file : (an existing file name)
		Unknown
	track_file : (an existing file name)
		Unknown
