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Manpage of sflutgen
sflutgen
Section: User Commands (1)
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NAME
sflutgen - Generates PICo lookup tables (LUT) for multi-fibre methods such as PASMRI and Q-Ball.
SYNOPSIS
sflutgen
-infofile <filename> -outputfilestem <filename stem> [options]
DESCRIPTION
sflutgen creates the lookup tables for the generalized multi-fibre implementation of the PICo tractography algorithm. The outputs of this program are either surface or line coefficients up to a given order. The calibration can be performed for different distributions, such as the Bingham and Watson distributions.
EXAMPLES
This methods uses data from the sfpicocalibrationdata program for calibration. The data is then reconstructed and the fibre-orientation estimates are calculated. The example below uses PASMRI to reconstruct and stores a maximum of 3 fibre-orientation estimates
sfpicocalibdata -schemefile A.scheme -infooutputfile A.info > PICo_data.Bfloat
mesd -schemefile A.scheme -filter PAS 1.4 < PICo_data.Bfloat | sfpeaks -inputmodel maxent -filter PAS 1.4 > PAS_Peaks.Bdouble
Once the calibration data has been calculated, lut's can be generated using the command
sflutgen -infofile A.info -outputstem PAS_lut < PAS_Peaks.Bdouble
This command is equavalent to
sflutgen -infofile A.info -outputstem PAS_lut -pdf bingham < PAS_Peaks.Bdouble
These commands will give you two lut's, one called PAS_lut_oneFibreSurfaceCoeffs.Bdouble and the other called PAS_lut_twoFibreSurfaceCoeffs.Bdouble
Each of these files contains big-endian doubles as standard. The format of the output is:
dimensions (1 for Watson, 2 for Bingham)
order (the order of the polynomial)
coefficient_1
coefficient_2
...
coefficient_N
In the case of the Watson, there is a single set of coefficients, which are ordered: constant, x, x^2, ..., x^order. In the case of the Bingham, there are two sets of coefficients (one for each surface), ordered so that
for j = 1 to order
for k = 1 to order
coeff_i = x^j * y^k
where j+k < order
OPTIONS
sflutgen flags
- -inputfile <input filename>
-
See modelfit(1).
- -outputfilestem <output filename>
-
This option allows you to define the name of the generated luts. The form of the filenames will be [stem]_oneFibreLUT.Bdouble and [stem]_twoFibreLUT.Bdouble
- -pdf <watson | bingham>
-
Sets the distribution to use for the calibration. The default is the Bingham distribution, which allows elliptical probability density contours. Currently
supported options are:
bingham - The Bingham distributionn, which allows elliptical probability density contours.
watson - The Watson distribution. This distribution is rotationally symmetric.
- -binincsize <bin increment size>
-
Sets the size of the bins. In the case of 2D histograms such as the Bingham, the bins are always square. Default is 1.
- -minvectsperbin <minimum direction vectors per bin>
-
Specifies the minimum number of fibre-orientation estimates a bin must contain before it is used in the lut line/surface generation. Default is 50. If you get the error "no fibre-orientation estimates in histogram!", the calibration data set is too small to get enough samples in any of the histogram bins. You can decrease the minimum number per bin to get things running in quick tests, but the statistics will not be reliable and for serious applications, you need to increase the size of the calibration data set until the error goes.
- -directmap
-
Use direct mapping between the eigenvalues and the distribution parameters instead of the log of the eigenvalues
- -infofile <Information file filename>
-
The Info file that corresponds to the calibration datafile used in the reconstruction.
AUTHORS
Kiran K Seunarine <camino@cs.ucl.ac.uk>
SEE ALSO
sfpeaks(1), sfpicocalibrationdata(1), picopdfs(1), track(1)
BUGS
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- EXAMPLES
-
- OPTIONS
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
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