interfaces.mrtrix.tensors

ConstrainedSphericalDeconvolution

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Wraps command csdeconv

Perform non-negativity constrained spherical deconvolution.

Note that this program makes use of implied symmetries in the diffusion profile. First, the fact the signal attenuation profile is real implies that it has conjugate symmetry, i.e. Y(l,-m) = Y(l,m)* (where * denotes the complex conjugate). Second, the diffusion profile should be antipodally symmetric (i.e. S(x) = S(-x)), implying that all odd l components should be zero. Therefore, this program only computes the even elements. Note that the spherical harmonics equations used here differ slightly from those conventionally used, in that the (-1)^m factor has been omitted. This should be taken into account in all subsequent calculations. Each volume in the output image corresponds to a different spherical harmonic component, according to the following convention:

  • [0] Y(0,0)
  • [1] Im {Y(2,2)}
  • [2] Im {Y(2,1)}
  • [3] Y(2,0)
  • [4] Re {Y(2,1)}
  • [5] Re {Y(2,2)}
  • [6] Im {Y(4,4)}
  • [7] Im {Y(4,3)}

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> csdeconv = mrt.ConstrainedSphericalDeconvolution()
>>> csdeconv.inputs.in_file = 'dwi.mif'
>>> csdeconv.inputs.encoding_file = 'encoding.txt'
>>> csdeconv.run()                                          

Inputs:

[Mandatory]
in_file: (an existing file name)
        diffusion-weighted image
        flag: %s, position: -3
response_file: (an existing file name)
        the diffusion-weighted signal response function for a single fibre
        population (see EstimateResponse)
        flag: %s, position: -2

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
debug: (a boolean)
        Display debugging messages.
        flag: -debug
directions_file: (an existing file name)
        a text file containing the [ el az ] pairs for the directions:
        Specify the directions over which to apply the non-negativity
        constraint (by default, the built-in 300 direction set is used)
        flag: -directions %s, position: -2
encoding_file: (an existing file name)
        Gradient encoding, supplied as a 4xN text file with each line is in
        the format [ X Y Z b ], where [ X Y Z ] describe the direction of
        the applied gradient, and b gives the b-value in units (1000
        s/mm^2). See FSL2MRTrix
        flag: -grad %s, position: 1
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
filter_file: (an existing file name)
        a text file containing the filtering coefficients for each even
        harmonic order.the linear frequency filtering parameters used for
        the initial linear spherical deconvolution step (default = [ 1 1 1 0
        0 ]).
        flag: -filter %s, position: -2
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
iterations: (an integer (int or long))
        the maximum number of iterations to perform for each voxel (default
        = 50)
        flag: -niter %s
lambda_value: (a float)
        the regularisation parameter lambda that controls the strength of
        the constraint (default = 1.0).
        flag: -lambda %s
mask_image: (an existing file name)
        only perform computation within the specified binary brain mask
        image
        flag: -mask %s, position: 2
maximum_harmonic_order: (an integer (int or long))
        set the maximum harmonic order for the output series. By default,
        the program will use the highest possible lmax given the number of
        diffusion-weighted images.
        flag: -lmax %s
normalise: (a boolean)
        normalise the DW signal to the b=0 image
        flag: -normalise, position: 3
out_filename: (a file name)
        Output filename
        flag: %s, position: -1
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
threshold_value: (a float)
        the threshold below which the amplitude of the FOD is assumed to be
        zero, expressed as a fraction of the mean value of the initial FOD
        (default = 0.1)
        flag: -threshold %s

Outputs:

spherical_harmonics_image: (an existing file name)
        Spherical harmonics image

DWI2SphericalHarmonicsImage

Link to code

Wraps command dwi2SH

Convert base diffusion-weighted images to their spherical harmonic representation.

This program outputs the spherical harmonic decomposition for the set measured signal attenuations. The signal attenuations are calculated by identifying the b-zero images from the diffusion encoding supplied (i.e. those with zero as the b-value), and dividing the remaining signals by the mean b-zero signal intensity. The spherical harmonic decomposition is then calculated by least-squares linear fitting. Note that this program makes use of implied symmetries in the diffusion profile.

First, the fact the signal attenuation profile is real implies that it has conjugate symmetry, i.e. Y(l,-m) = Y(l,m)* (where * denotes the complex conjugate). Second, the diffusion profile should be antipodally symmetric (i.e. S(x) = S(-x)), implying that all odd l components should be zero. Therefore, this program only computes the even elements.

Note that the spherical harmonics equations used here differ slightly from those conventionally used, in that the (-1)^m factor has been omitted. This should be taken into account in all subsequent calculations.

Each volume in the output image corresponds to a different spherical harmonic component, according to the following convention:

  • [0] Y(0,0)
  • [1] Im {Y(2,2)}
  • [2] Im {Y(2,1)}
  • [3] Y(2,0)
  • [4] Re {Y(2,1)}
  • [5] Re {Y(2,2)}
  • [6] Im {Y(4,4)}
  • [7] Im {Y(4,3)}

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> dwi2SH = mrt.DWI2SphericalHarmonicsImage()
>>> dwi2SH.inputs.in_file = 'diffusion.nii'
>>> dwi2SH.inputs.encoding_file = 'encoding.txt'
>>> dwi2SH.run()                                    

Inputs:

[Mandatory]
encoding_file: (an existing file name)
        Gradient encoding, supplied as a 4xN text file with each line is in
        the format [ X Y Z b ], where [ X Y Z ] describe the direction of
        the applied gradient, and b gives the b-value in units (1000
        s/mm^2). See FSL2MRTrix
        flag: -grad %s, position: 1
in_file: (an existing file name)
        Diffusion-weighted images
        flag: %s, position: -2

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
maximum_harmonic_order: (a float)
        set the maximum harmonic order for the output series. By default,
        the program will use the highest possible lmax given the number of
        diffusion-weighted images.
        flag: -lmax %s
normalise: (a boolean)
        normalise the DW signal to the b=0 image
        flag: -normalise, position: 3
out_filename: (a file name)
        Output filename
        flag: %s, position: -1
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

spherical_harmonics_image: (an existing file name)
        Spherical harmonics image

Directions2Amplitude

Link to code

Wraps command dir2amp

convert directions image to amplitudes

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> amplitudes = mrt.Directions2Amplitude()
>>> amplitudes.inputs.in_file = 'peak_directions.mif'
>>> amplitudes.run()                                          

Inputs:

[Mandatory]
in_file: (an existing file name)
        the input directions image. Each volume corresponds to the x, y & z
        component of each direction vector in turn.
        flag: %s, position: -2

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
display_debug: (a boolean)
        Display debugging messages.
        flag: -debug
display_info: (a boolean)
        Display information messages.
        flag: -info
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
num_peaks: (an integer (int or long))
        the number of peaks to extract (default is 3)
        flag: -num %s
out_file: (a file name)
        the output amplitudes image
        flag: %s, position: -1
peak_directions: (a list of from 2 to 2 items which are a float)
        phi theta. the direction of a peak to estimate. The algorithm will
        attempt to find the same number of peaks as have been specified
        using this option phi: the azimuthal angle of the direction (in
        degrees). theta: the elevation angle of the direction (in degrees,
        from the vertical z-axis)
        flag: -direction %s
peaks_image: (an existing file name)
        the program will try to find the peaks that most closely match those
        in the image provided
        flag: -peaks %s
quiet_display: (a boolean)
        do not display information messages or progress status.
        flag: -quiet
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_file: (an existing file name)
        amplitudes image

EstimateResponseForSH

Link to code

Wraps command estimate_response

Estimates the fibre response function for use in spherical deconvolution.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> estresp = mrt.EstimateResponseForSH()
>>> estresp.inputs.in_file = 'dwi.mif'
>>> estresp.inputs.mask_image = 'dwi_WMProb.mif'
>>> estresp.inputs.encoding_file = 'encoding.txt'
>>> estresp.run()                                   

Inputs:

[Mandatory]
encoding_file: (an existing file name)
        Gradient encoding, supplied as a 4xN text file with each line is in
        the format [ X Y Z b ], where [ X Y Z ] describe the direction of
        the applied gradient, and b gives the b-value in units (1000
        s/mm^2). See FSL2MRTrix
        flag: -grad %s, position: 1
in_file: (an existing file name)
        Diffusion-weighted images
        flag: %s, position: -3
mask_image: (an existing file name)
        only perform computation within the specified binary brain mask
        image
        flag: %s, position: -2

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
debug: (a boolean)
        Display debugging messages.
        flag: -debug
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
maximum_harmonic_order: (an integer (int or long))
        set the maximum harmonic order for the output series. By default,
        the program will use the highest possible lmax given the number of
        diffusion-weighted images.
        flag: -lmax %s
normalise: (a boolean)
        normalise the DW signal to the b=0 image
        flag: -normalise
out_filename: (a file name)
        Output filename
        flag: %s, position: -1
quiet: (a boolean)
        Do not display information messages or progress status.
        flag: -quiet
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

response: (an existing file name)
        Spherical harmonics image

FindShPeaks

Link to code

Wraps command find_SH_peaks

identify the orientations of the N largest peaks of a SH profile

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> shpeaks = mrt.FindShPeaks()
>>> shpeaks.inputs.in_file = 'csd.mif'
>>> shpeaks.inputs.directions_file = 'dirs.txt'
>>> shpeaks.inputs.num_peaks = 2
>>> shpeaks.run()                                          

Inputs:

[Mandatory]
directions_file: (an existing file name)
        the set of directions to use as seeds for the peak finding
        flag: %s, position: -2
in_file: (an existing file name)
        the input image of SH coefficients.
        flag: %s, position: -3

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
display_debug: (a boolean)
        Display debugging messages.
        flag: -debug
display_info: (a boolean)
        Display information messages.
        flag: -info
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
num_peaks: (an integer (int or long))
        the number of peaks to extract (default is 3)
        flag: -num %s
out_file: (a file name)
        the output image. Each volume corresponds to the x, y & z component
        of each peak direction vector in turn
        flag: %s, position: -1
peak_directions: (a list of from 2 to 2 items which are a float)
        phi theta. the direction of a peak to estimate. The algorithm will
        attempt to find the same number of peaks as have been specified
        using this option phi: the azimuthal angle of the direction (in
        degrees). theta: the elevation angle of the direction (in degrees,
        from the vertical z-axis)
        flag: -direction %s
peak_threshold: (a float)
        only peak amplitudes greater than the threshold will be considered
        flag: -threshold %s
peaks_image: (an existing file name)
        the program will try to find the peaks that most closely match those
        in the image provided
        flag: -peaks %s
quiet_display: (a boolean)
        do not display information messages or progress status.
        flag: -quiet
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_file: (an existing file name)
        Peak directions image

GenerateDirections

Link to code

Wraps command gendir

generate a set of directions evenly distributed over a hemisphere.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> gendir = mrt.GenerateDirections()
>>> gendir.inputs.num_dirs = 300
>>> gendir.run()                                          

Inputs:

[Mandatory]
num_dirs: (an integer (int or long))
        the number of directions to generate.
        flag: %s, position: -2

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
display_debug: (a boolean)
        Display debugging messages.
        flag: -debug
display_info: (a boolean)
        Display information messages.
        flag: -info
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
niter: (an integer (int or long))
        specify the maximum number of iterations to perform.
        flag: -niter %s
out_file: (a file name)
        the text file to write the directions to, as [ az el ] pairs.
        flag: %s, position: -1
power: (a float)
        specify exponent to use for repulsion power law.
        flag: -power %s
quiet_display: (a boolean)
        do not display information messages or progress status.
        flag: -quiet
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_file: (an existing file name)
        directions file

concat_files()

Link to code