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interfaces.camino.odf

LinRecon

Link to code

Wraps command linrecon

Runs a linear transformation in each voxel.

Reads a linear transformation from the matrix file assuming the imaging scheme specified in the scheme file. Performs the linear transformation on the data in every voxel and outputs the result to the standard output. The ouput in every voxel is actually:

[exit code, ln(S(0)), p1, ..., pR]

where p1, ..., pR are the parameters of the reconstruction. Possible exit codes are:

0. No problems. 6. Bad data replaced by substitution of zero.

The matrix must be R by N+M where N+M is the number of measurements and R is the number of parameters of the reconstruction. The matrix file contains binary double-precision floats. The matrix elements are stored row by row.

Example

First run QBallMX and create a linear transform matrix using Spherical Harmonics (sh).

>>> import nipype.interfaces.camino as cam
>>> qballmx = cam.QBallMX()
>>> qballmx.inputs.scheme_file = 'A.scheme'
>>> qballmx.inputs.basistype = 'sh'
>>> qballmx.inputs.order = 4
>>> qballmx.run()            

Then run it over each voxel using LinRecon

>>> qballcoeffs = cam.LinRecon()
>>> qballcoeffs.inputs.in_file = 'SubjectA.Bfloat'
>>> qballcoeffs.inputs.scheme_file = 'A.scheme'
>>> qballcoeffs.inputs.qball_mat = 'A_qmat.Bdouble'
>>> qballcoeffs.inputs.normalize = True
>>> qballcoeffs.run()         

Inputs:

[Mandatory]
in_file: (an existing file name)
        voxel-order data filename
qball_mat: (an existing file name)
        Linear transformation matrix.
scheme_file: (an existing file name)
        Specifies the scheme file for the diffusion MRI data
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
bgmask: (an existing file name)
        background mask
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', 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
in_file: (an existing file name)
        voxel-order data filename
log: (a boolean)
        Transform the log measurements rather than the measurements
        themselves
normalize: (a boolean)
        Normalize the measurements and discard the zero measurements before
        the linear transform.
out_file: (a file name)
qball_mat: (an existing file name)
        Linear transformation matrix.
scheme_file: (an existing file name)
        Specifies the scheme file for the diffusion MRI data
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

recon_data: (an existing file name)
        Transformed data

QBallMX

Link to code

Wraps command qballmx

Generates a reconstruction matrix for Q-Ball. Used in LinRecon with the same scheme file to reconstruct data.

Example 1

To create a linear transform matrix using Spherical Harmonics (sh).

>>> import nipype.interfaces.camino as cam
>>> qballmx = cam.QBallMX()
>>> qballmx.inputs.scheme_file = 'A.scheme'
>>> qballmx.inputs.basistype = 'sh'
>>> qballmx.inputs.order = 6
>>> qballmx.run()            

Example 2

To create a linear transform matrix using Radial Basis Functions (rbf). This command uses the default setting of rbf sigma = 0.2618 (15 degrees), data smoothing sigma = 0.1309 (7.5 degrees), rbf pointset 246

>>> import nipype.interfaces.camino as cam
>>> qballmx = cam.QBallMX()
>>> qballmx.inputs.scheme_file = 'A.scheme'
>>> qballmx.run()              

The linear transform matrix from any of these two examples can then be run over each voxel using LinRecon

>>> qballcoeffs = cam.LinRecon()
>>> qballcoeffs.inputs.in_file = 'SubjectA.Bfloat'
>>> qballcoeffs.inputs.scheme_file = 'A.scheme'
>>> qballcoeffs.inputs.qball_mat = 'A_qmat.Bdouble'
>>> qballcoeffs.inputs.normalize = True
>>> qballcoeffs.inputs.bgmask = 'brain_mask.nii'
>>> qballcoeffs.run()             

Inputs:

[Mandatory]
scheme_file: (an existing file name)
        Specifies the scheme file for the diffusion MRI data
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
basistype: ('rbf' or 'sh', nipype default value: rbf)
        Basis function type. "rbf" to use radial basis functions "sh" to use
        spherical harmonics
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', 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
order: (an integer)
        Specific to sh. Maximum order of the spherical harmonic series.
        Default is 4.
out_file: (a file name)
rbfpointset: (an integer)
        Specific to rbf. Sets the number of radial basis functions to use.
        The value specified must be present in the Pointsets directory. The
        default value is 246.
rbfsigma: (a float)
        Specific to rbf. Sets the width of the interpolating basis
        functions. The default value is 0.2618 (15 degrees).
scheme_file: (an existing file name)
        Specifies the scheme file for the diffusion MRI data
smoothingsigma: (a float)
        Specific to rbf. Sets the width of the smoothing basis functions.
        The default value is 0.1309 (7.5 degrees).
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

qmat: (an existing file name)
        Q-Ball reconstruction matrix

SFPeaks

Link to code

Wraps command sfpeaks

Finds the peaks of spherical functions.

This utility reads coefficients of the spherical functions and outputs a list of peak directions of the function. It computes the value of the function at each of a set of sample points. Then it finds local maxima by finding all points at which the function is larger than for any other point within a fixed search radius (the default is 0.4). The utility then uses Powell’s algorithm to optimize the position of each local maximum. Finally the utility removes duplicates and tiny peaks with function value smaller than some threshold, which is the mean of the function plus some number of standard deviations. By default the program checks for con- sistency with a second set of starting points, but skips the optimization step. To speed up execution, you can turn off the con- sistency check by setting the noconsistencycheck flag to True.

By default, the utility constructs a set of sample points by randomly rotating a unit icosahedron repeatedly (the default is 1000 times, which produces a set of 6000 points) and concatenating the lists of vertices. The ‘pointset = <index>’ attribute can tell the utility to use an evenly distributed set of points (index 0 gives 1082 points, 1 gives 1922, 2 gives 4322, 3 gives 8672, 4 gives 15872, 5 gives 32762, 6 gives 72032), which is quicker, because you can get away with fewer points. We estimate that you can use a factor of 2.5 less evenly distributed points than randomly distributed points and still expect similar performance levels.

The output for each voxel is: - exitcode (inherited from the input data). - ln(A(0)) - number of peaks found. - flag for consistency with a repeated run (number of directions is

the same and the directions are the same to within a threshold.)
  • mean(f).
  • std(f).
  • direction 1 (x, y, z, f, H00, H01, H10, H11).
  • direction 2 (x, y, z, f, H00, H01, H10, H11).
  • direction 3 (x, y, z, f, H00, H01, H10, H11).

H is the Hessian of f at the peak. It is the matrix: [d^2f/ds^2 d^2f/dsdt] [d^2f/dtds d^2f/dt^2] = [H00 H01]

[H10 H11]

where s and t are orthogonal coordinates local to the peak.

By default the maximum number of peak directions output in each voxel is three. If less than three directions are found, zeros are output for later directions. The peaks are ordered by the value of the function at the peak. If more than the maximum number of directions are found only the strongest ones are output. The maximum number can be changed setting the ‘numpds’ attribute.

The utility can read various kinds of spherical function, but must be told what kind of function is input using the ‘inputmodel’ attribute. The description of the ‘inputmodel’ attribute lists additional information required by SFPeaks for each input model.

Example

First run QBallMX and create a linear transform matrix using Spherical Harmonics (sh).

>>> import nipype.interfaces.camino as cam
>>> sf_peaks = cam.SFPeaks()
>>> sf_peaks.inputs.in_file = 'A_recon_params.Bdouble'
>>> sf_peaks.inputs.inputmodel = 'sh'
>>> sf_peaks.inputs.order = 4
>>> sf_peaks.inputs.density = 100
>>> sf_peaks.inputs.searchradius = 1.0
>>> sf_peaks.run()          

Inputs:

[Mandatory]
in_file: (an existing file name)
        Voxel-order data of spherical functions
inputmodel: ('sh' or 'maxent' or 'rbf')
        Type of functions input via in_file. Currently supported options
        are: sh - Spherical harmonic series. Specify the maximum order of
        the SH series with the "order" attribute if different from the
        default of 4. maxent - Maximum entropy representations output by
        MESD. The reconstruction directions input to MESD must be specified.
        By default this is the same set of gradient directions (excluding
        zero gradients) in the scheme file, so specify the "schemefile"
        attribute unless the "mepointset" attribute was set in MESD. rbf -
        Sums of radial basis functions. Specify the pointset with the
        attribute "rbfpointset" if different from the default. See QBallMX.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
density: (an integer)
        The number of randomly rotated icosahedra to use in constructing the
        set of points for random sampling in the peak finding algorithm.
        Default is 1000, which works well for very spiky maxent functions.
        For other types of function, it is reasonable to set the density
        much lower and increase the search radius slightly, which speeds up
        the computation.
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', 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
in_file: (an existing file name)
        Voxel-order data of spherical functions
inputmodel: ('sh' or 'maxent' or 'rbf')
        Type of functions input via in_file. Currently supported options
        are: sh - Spherical harmonic series. Specify the maximum order of
        the SH series with the "order" attribute if different from the
        default of 4. maxent - Maximum entropy representations output by
        MESD. The reconstruction directions input to MESD must be specified.
        By default this is the same set of gradient directions (excluding
        zero gradients) in the scheme file, so specify the "schemefile"
        attribute unless the "mepointset" attribute was set in MESD. rbf -
        Sums of radial basis functions. Specify the pointset with the
        attribute "rbfpointset" if different from the default. See QBallMX.
mepointset: (an integer)
        Use a set of directions other than those in the scheme file for the
        deconvolution kernel. The number refers to the number of directions
        on the unit sphere. For example, "mepointset = 54" uses the
        directions in "camino/PointSets/Elec054.txt" Use this option only if
        you told MESD to use a custom set of directions with the same
        option. Otherwise, specify the scheme file with the "schemefile"
        attribute.
noconsistencycheck: (a boolean)
        Turns off the consistency check. The output shows all consistencies
        as true.
numpds: (an integer)
        The largest number of peak directions to output in each voxel.
order: (an integer)
        Specific to sh. Maximum order of the spherical harmonic series.
out_file: (a file name)
pdthresh: (a float)
        Base threshold on the actual peak direction strength divided by the
        mean of the function. The default is 1.0 (the peak must be equal or
        greater than the mean).
pointset: (an integer)
        To sample using an evenly distributed set of points instead. The
        integer can be 0, 1, ..., 7. Index 0 gives 1082 points, 1 gives
        1922, 2 gives 3002, 3 gives 4322, 4 gives 5882, 5 gives 8672, 6
        gives 12002, 7 gives 15872.
rbfpointset: (an integer)
        Specific to rbf. Sets the number of radial basis functions to use.
        The value specified must be present in the Pointsets directory. The
        default value is 246.
scheme_file: (an existing file name)
        Specific to maxent. Specifies the scheme file.
searchradius: (a float)
        The search radius in the peak finding algorithm. The default is 0.4
        (cf. "density")
stdsfrommean: (a float)
        This is the number of standard deviations of the function to be
        added to the "pdthresh" attribute in the peak directions pruning.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

peaks: (an existing file name)
        Peaks of the spherical functions.