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sfpicocalibdata

Section: User Commands (1)
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NAME

sfpicocalibdata - Generates Spherical Function PICo Calibration Data

SYNOPSIS

sfpicocalibdata -snr <S> -schemefile <Scheme file name> -infooutputfile <information output filename> [options]

DESCRIPTION

sfpicocalibdata creates synthetic data for use with sflutgen. The synthetic data is generated using a mixture of gaussians, in the same way datasynth generates data. Each voxel of data models a slightly different fibre configuration (varying fractional anisotrpy and fibre-crossings) and undergoes a random rotation to help account for any directional bias in the chosen acquisition scheme. A second file, which stores information about the datafile, is generated along with the datafile.

EXAMPLES

To create a calibration dataset using the default settings, use the command

sfpicocalibdata -snr 20 -schemefile A.scheme -infooutputfile PICo_data.info > PICo_data.Bfloat

The default settings create a large dataset (249,231 voxels), of which 3401 voxels contain a single fibre population per voxel and the rest of the voxels contain two fibre-populations. The amount of data produced can be varied by specifying the ranges and steps of the parameters for both the one and two fibre datasets used. For example, the command

sfpicocalibdata -schemefile A.scheme -snr 20 -infooutputfile PICO_data.info -twodtfarange 0.3 0.9 -twodtfastep 0.02 -twodtanglerange 0 0.785 -twodtanglestep 0.03925 -twodtmixmax 0.8 -twodtmixstep 0.1 > PICO_data.Bfloat

would provide 76,313 voxels of synthetic data, where 3401 voxels simulate the one fibre cases and 72,912 voxels simulate the various two fibre cases. However, care should be taken to ensure that enough data is generated for calcuating the lut.

OPTIONS

sfpicocalibdata processes options in command line order.

-inputfile <input filename>: See modelfit(1).
-outputfilestem <output filename>: See modelfit(1).
-schemefile <Scheme file name>: See modelfit(1).
-infooutputfile <information output filename>: The name to be given to the information output filename.
-trace <the trace>: See datasynth(1).
-onedtfarange <the fa range for the single tensor case>: This flag is used to provide the minimum and maximum fa for the single tensor synthetic data
-onedtfastep <the fa step size for the single tensor>: controls how many steps there are between the minimum and maximum fa settings
-twodtfarange <the fa range for the two tensor case>: This flag is used to provide the minimum and maximum fa for the two tensor synthetic data. The fa is varied for both tensors to give all the different permutations
-twodtfastep <the fa step size for the two tensor case>: controls how many steps there are between the minimum and maximum fa settings for the two tensor cases
-twodtanglerange <the crossing angle range for the two fibre cases>: Use this flag to specify the minimum and maximum crossing angles between the two fibres
-twodtanglestep <the crossing angle step size>: controls how many steps there are between the minimum and maximum crossing angles for the two tensor cases
-twodtmixmax <mixing parameter>: controls the proportion of one fibre population to the other. the minimum mixing parameter is (1 - twodtmixmax)
-twodtmixstep <the mixing parameter step size for the two tensor case>: Used to specify how many mixing parameter increments to use
-snr <S>: See datasynth(1).
-seed <seed>: See datasynth(1).

AUTHORS

Phil Cook <camino@cs.ucl.ac.uk> Kiran K Seunarine <camino@cs.ucl.ac.uk>

BUGS

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

Sfpicocalibdata