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consfrac

Section: User Commands (1)
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NAME

consfrac - Computes the consistency fraction for multiple fibre reconstructions.

SYNOPSIS

consfrac -voxels <num voxels> [options]

DESCRIPTION

Reads in the output of sfpeaks and computes the consistency fraction with a known set of expected peak directions. Used for performance evaluations of multiple-fibre reconstructions in simulation.

The consistency fraction is the fraction of trials in which the sfpeaks output is consistent with a known set of expected peak directions. Two sets of directions are consistent if they contain the same number of directions and each element of one set is within a small angular tolerance of an element of the other and vice versa. (Defined in Jansons and Alexander, Inverse Problems 19 2004.)

The program outputs three numbers:

- the number of input voxels
- the number of "successful" trials (which is the number with the expected number of peaks) and,

- the consistency fraction itself}.

EXAMPLES

Here are some examples using q-ball.

qballmx -schemefile test/bmx7.scheme > /tmp/BMX7_QBMX.Bdouble

datasynth -voxels 20 -testfunc 1 -schemefile test/bmx7.scheme -snr 16 | linrecon - test/bmx7.scheme /tmp/BMX7_QBMX.Bdouble -normalize | sfpeaks -inputmodel rbf -rbfpointset 246 -density 100 | consfrac -testfunc 1 -voxels 20 | double2txt

Outputs the following:

2.000000E01    Number of trials

1.000000E00    Fraction of successful trials (with the right number of peaks)

1.000000E00    Consistency fraction

Increasing the noise level reduces the consistency fraction, as some peak directions are too far from the expected direction:

datasynth -voxels 20 -testfunc 1 -schemefile test/bmx7.scheme -snr 4 | linrecon - test/bmx7.scheme /tmp/BMX7_QBMX.Bdouble -normalize | sfpeaks -inputmodel rbf -rbfpointset 246 -density 100 | consfrac -testfunc 1 -voxels 20 | double2txt

2.000000E01
1.000000E00
3.500000E-01

The following is a simple investigation of how the consistency fraction varies with noise level. This time we use a test function with two directions, which q-ball finds harder to reconstruct. Note how shredder pulls out the third number from each output, which is the consistency fraction.

for snr in 4 8 12 16 20 24 28 32; do echo SNR is $snr C is; datasynth -voxels 20 -testfunc 3 -schemefile test/bmx7.scheme -snr $snr | linrecon - test/bmx7.scheme /tmp/BMX7_QBMX.Bdouble -normalize | sfpeaks -inputmodel rbf -rbfpointset 246 -density 100 | consfrac -testfunc 3 -voxels 20 | shredder $((8*2)) 8 $((8*6)) | double2txt; done

SNR is 4 C is
5.000000E-02
SNR is 8 C is
5.000000E-01
SNR is 12 C is
7.500000E-01
SNR is 16 C is
1.000000E00
SNR is 20 C is
1.000000E00
SNR is 24 C is
1.000000E00
SNR is 28 C is
1.000000E00
SNR is 32 C is
1.000000E00

Here is a similar example using PASMRI:

for snr in 4 8 12 16 20 24 28 32; do echo SNR is $snr C is; datasynth -voxels 20 -testfunc 3 -schemefile test/bmx7.scheme -snr $snr | mesd -filter PAS 1.4 -schemefile test/bmx7.scheme | sfpeaks -inputmodel maxent -mepointset 54 | consfrac -testfunc 3 -voxels 20 | shredder $((8*2)) 8 $((8*6)) | double2txt; done

SNR is 4 C is
3.500000E-01
SNR is 8 C is
9.000000E-01
SNR is 12 C is
1.000000E00
SNR is 16 C is
1.000000E00
SNR is 20 C is
1.000000E00
SNR is 24 C is
1.000000E00
SNR is 28 C is
1.000000E00
SNR is 32 C is
1.000000E00

OPTIONS

Standard IO options, as listed in modelfit(1).

Standard synthetic data options to specify the known set of directions, eg -testfunc, -rotation, -dt2rotangle, etc, as listed in datasynth(1).

-voxels <number of voxels>

The number of voxels in the input data. Defaults to one, so must be specified.

-numpds <index>

The number of principal directions per voxel in the input (ie, output of sfpeaks(1)). The default is 3, as in sfpeaks(1).

-thresh <index>

The threshold on the absolute dot product of two directions above which they are considered consistent. The default is 0.95.

AUTHORS

Daniel Alexander <camino@cs.ucl.ac.uk>

BUGS

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

Consfrac