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ballstickfit

Section: User Commands (1)
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NAME

ballstickfit - Fits a partial volume model to diffusion MRI measurements.

SYNOPSIS

ballstickfit <data file> <scheme file> [options]

DESCRIPTION

Reads diffusion MRI data, acquired using the acquisition scheme detailed in the scheme file, and fits the e ball and stick partial volume model [Behrens et al, MRM 50:1077-1088, (2003)].

For help with scheme files, please see the section "scheme files" in camino(1).

The data file stores the diffusion MRI data in voxel order with the measurements stored as big-endian four-byte floats and ordered as in the scheme file. See modelfit(1) and camino(1) for the format of the data file and scheme file. The program fits the diffusion tensor to each voxel and outputs the results, in voxel order and as big-endian eight-byte doubles, to the standard output. The program outputs eight values in each voxel: [exitcode, ln(S(0)), d, f, vx, vy, vz]. The model, as parameterized in Friman et al, IEEE-TMI 25:965-978 (2006), is

S(g_i, b_i) = S(0) [ (1-f) exp(-b_i d) + f exp(-b_i d [g.v]^2) ]

where the wavenumber of measurement i is q_i, the gradient direction g_i = q_i / |q_i|, and the b-value b_i is |q_i|^2 t, where t is the diffusion time. The measured signal is modelled as a combination of isotropic diffusion (the ball) and diffusion along the axis v=[vx, vy, vz] (the stick). The two compartments share a common diffusion coefficient, d.

The model parameters are fit to the data using Levenberg-Marquardt optimization. An exit code of zero indicates no problems. For a list of other exit codes, see modelfit(1). An exit code of 2 indicates an optimization failure; in this case a linear DT fit is substituted: f is set to the fractional anisotropy of the DT, d is set to tr(D) / 3, and v is the principal eigenvector of the tensor.

This program is a simplified wrapper to modelfit. The command

ballstickfit SubjectA.Bfloat A.scheme

is equivalent to

modelfit -inputfile SubjectA.Bfloat -schemefile A.scheme -inversion -3

To read data from stdin, do:

cat <data file> | ballstickfit - A.scheme

EXAMPLES

cat SubjectA.Bfloat | ballstickfit - A.scheme > ballstick.Bdouble

pdview -inputmodel ballstick -inputfile ballstick.Bdouble

AUTHORS

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

BUGS

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Ballstickfit