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nipype.interfaces.diffusion_toolkit.odf
=======================================


:class:`HARDIMat`
-----------------


Wraps command **hardi_mat**

Use hardi_mat to calculate a reconstruction matrix from a gradient table

Inputs:: 

	[Mandatory]
	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
	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_info : (an existing file name)
		specify image information file. the image info file is generated
        from original dicom image by diff_unpack program and contains image
        orientation and other information needed for reconstruction and
        tracking. by default will look into the image folder for .info file
	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
	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
	odf_file : (an existing file name)
		filename that contains the reconstruction points on a HEMI-sphere.
        use the pre-set 181 points by default
	order : (an integer)
		maximum order of spherical harmonics. must be even number. default
        is 4
	out_file : (a file name)
		output matrix file
	reference_file : (an existing file name)
		provide a dicom or nifti image as the reference for the program to
        figure out the image orientation information. if no such info was
        found in the given image header, the next 5 options -info, etc.,
        will be used if provided. if image orientation info can be found
        in the given reference, all other 5 image orientation options will 
        be IGNORED


Outputs:: 

	out_file : (an existing file name)
		output matrix file

:class:`ODFRecon`
-----------------


Wraps command **odf_recon**

Use odf_recon to generate tensors and other maps

Inputs:: 

	[Mandatory]
	DWI : (an existing file name)
		Input raw data
	matrix : (an existing file name)
		use given file as reconstruction matrix.
	n_b0 : (an integer)
		number of b0 scans. by default the program gets this information
        from the number of directions and number of volumes in
        the raw data. useful when dealing with incomplete raw
        data set or only using part of raw data set to reconstruct
	n_directions : (an integer)
		Number of directions
	n_output_directions : (an integer)
		Number of output directions

	[Optional]
	args : (a string)
		Additional parameters to the command
	dsi : (a boolean)
		indicates that the data is dsi
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	filter : (a boolean)
		apply a filter (e.g. high pass) to the raw image
	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
	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_entropy : (a boolean)
		output entropy map
	output_type : ('nii' or 'analyze' or 'ni1' or 'nii.gz')
		output file type
	sharpness : (a float)
		smooth or sharpen the raw data. factor > 0 is smoothing.
        factor < 0 is sharpening. default value is 0
        NOTE: this option applies to DSI study only
	subtract_background : (a boolean)
		subtract the background value before reconstruction


Outputs:: 

	B0 : (an existing file name)
		Unknown
	DWI : (an existing file name)
		Unknown
	ODF : (an existing file name)
		Unknown
	entropy : (a file name)
		Unknown
	max : (an existing file name)
		Unknown

:class:`ODFTracker`
-------------------


Wraps command **odf_tracker**

Use odf_tracker to generate track file

Inputs:: 

	[Mandatory]
	ODF : (an existing file name)
		Unknown
	mask1_file : (a file name)
		first mask image
	max : (an existing file name)
		Unknown

	[Optional]
	angle_threshold : (a float)
		set angle threshold. default value is 35 degree for
        default tracking method and 25 for rk2
	args : (a string)
		Additional parameters to the command
	disc : (a boolean)
		use disc tracking
	dsi : (a boolean)
		 specify the input odf data is dsi. because dsi recon uses fixed
        pre-calculated matrix, some special orientation patch needs to
        be applied to keep dti/dsi/q-ball consistent.
	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
	input_data_prefix : (a string)
		recon data prefix
	input_output_type : ('nii' or 'analyze' or 'ni1' or 'nii.gz')
		input and output file type
	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
	limit : (an integer)
		in some special case, such as heart data, some track may go into
        infinite circle and take long time to stop. this option allows
        setting a limit for the longest tracking steps (voxels)
	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
	out_file : (a file name)
		output track file
	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
	runge_kutta2 : (a boolean)
		use 2nd order runge-kutta method for tracking.
        default tracking method is non-interpolate streamline
	slice_order : (an integer)
		set the slice order. 1 means normal, -1 means reversed. default value is 1
	step_length : (a float)
		set step length, in the unit of minimum voxel size.
        default value is 0.1.
	swap_xy : (a boolean)
		swap x and y vectors while tracking
	swap_yz : (a boolean)
		swap y and z vectors while tracking
	swap_zx : (a boolean)
		swap x and z vectors while tracking
	voxel_order : ('RAS' or 'RPS' or 'RAI' or 'RPI' or 'LAI' or 'LAS' or 'LPS' or 'LPI')
		specify the voxel order in RL/AP/IS (human brain) reference. must be
        3 letters with no space in between.
        for example, RAS means the voxel row is from L->R, the column
        is from P->A and the slice order is from I->S.
        by default voxel order is determined by the image orientation
        (but NOT guaranteed to be correct because of various standards).
        for example, siemens axial image is LPS, coronal image is LIP and
        sagittal image is PIL.
        this information also is NOT needed for tracking but will be saved
        in the track file and is essential for track display to map onto
        the right coordinates


Outputs:: 

	track_file : (an existing file name)
		output track file
