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 sfpicocalibdata 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
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
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.
