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picocalibdata

Section: User Commands (1)
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NAME

picocalibdata - Creates synthetic data for PICo calibration

SYNOPSIS

picocalibdata -snr <value> -schemefile <file> [options]

DESCRIPTION

picocalibdata generates synthetic diffusion MRI data from a range of test functions, using the specified acquisition scheme and SNR.

The program is part of the spherical-function PICo calibration routine. To calibrate PICo for diffusion tensors, see dtlutgen(1).

picocalibdata outputs a single voxel of synthetic data from a range of test functions. The single-fibre test functions are zero mean Gaussian (see datasynth(1)): G(.; D_1, tau), where tau is the diffusion time specified in the scheme file, and the tensor is

D_1 = diag((T-l_1)/2, (T-l_1)/2, l_1) .

By default, the program generates data from a range of test functions, where first eigenvalue l_1 varies such that the fractional anisotropy of D_1 ranges between 0.1 and 0.9. The trace of the tensor is T = 21 * 10^{-10} m^2 s^{-1} by default.

A different random rotation is applied to each D_1, so the test function is oriented randomly in each voxel.

The two-fibre test functions are

(1-a)*G(.; D_1, tau) + (a)*G(.; D_2, tau) ,

where 0.5 < a <= 1. The tensor D_2 is

D_2 = R^T * diag((T-m_1)/2, m_1, (T-m_1)/2) * R ,

where R is a rotation matrix, which specifies a rotation by an angle theta about the second eigenvector of D_1, so that the angle between the principal directions of D_1 and D_2 is (pi / 2 - theta).

By default, picocalibdata creates data from the two-fibre test function with many combinations of D_1 and D_2, such that the fractional anisotropy of D_1 and D_2 vary between 0.3 and 0.9, the angle theta varies between 0 and pi / 4, and the mixing parameter a varies between 0.5 and 0.8. A random rotation is applied to each test function before the data is generated.

The program outputs a text file containing information about the test functions used to generate the data. By default, this file is pico_calibration_info.txt.

EXAMPLES

Use the default parameters to generate data for a given scheme file, with an SNR of 20 in white matter in the unweighted image

picocalibdata -snr 20 -schemefile A.scheme > calib_data

Increase the range of single-fibre test functions and output text file to another location

picocalibdata -snr 20 -schemefile A.scheme -onedtfarange 0.1 0.9 -infooutputfile A_pico_calib.txt > calib_data

OPTIONS

-onedtfarange <min max>

Fractional anisotropy range of single-tensor test functions. Default is 0.1 0.9.

-onedtfastep <size>

The anisotropy of the single-tensor test functions increase in units of size from the minimum to the maximum. Default is 5E-4.

-twodtfarange <min max> Fractional anisotropy range of two-tensor test functions. Default is 0.3 0.9.

-twodtfastep <size>

The anisotropy of the two-tensor test functions increase in units of step from the minimum to the maximum. Default is 1E-2. Data is generated for each pair of tensors within the FA range - so if there are N steps of size from the minimum to maximum FA, then there will be N(N+1)/2 combinations of tensor anisotropy in the two-tensor test functions.

-twodtanglerange <min max>

The minimum and maximum rotation angle to apply to the second diffusion tensor, in radians. The angle between the principal directions of the diffusion tensors is pi / 2 - angle. The default range is 0 pi / 4.

-twodtanglesstep <size>

The rotation angle for the second diffusion tensor increases in units of size.

-twodtmixmax <max>

Maximum mixing parameter a, for two-tensor test functions: p = (1-a)*G(.; D_1, tau) + (a)*G(.; D_2, tau). Should be between 0.5 and 1.0. The minimum value of a is 1.0 - max.

-twodtmixstep <size>

The mixing parameter increases in units of size.

-snr <value>

The signal to noise ratio of the unweighted (q = 0) measurements.

-trace <value>

Trace of the diffusion tensor(s) used in the test functions. The default is 2100E-12 m^2 s^-1.

AUTHORS

Philip Cook <camino@cs.ucl.ac.uk>

BUGS

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Time: 02:07:11 GMT, December 04, 2017

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