csdeconv

Description

perform non-negativity constrained spherical deconvolution.

Note that this program makes use of implied symmetries in the diffusion profile. First, the fact the signal attenuation profile is real implies that it has conjugate symmetry, i.e. Y(l,-m) = Y(l,m)* (where * denotes the complex conjugate). Second, the diffusion profile should be antipodally symmetric (i.e. S(x) = S(-x)), implying that all odd l components should be zero. Therefore, this program only computes the even elements.

Note that the spherical harmonics equations used here differ slightly from those conventionally used, in that the (-1)^m factor has been omitted. This should be taken into account in all subsequent calculations.

Each volume in the output image corresponds to a different spherical harmonic component, according to the following convention:

[0] Y(0,0)

[1] Im {Y(2,2)}

[2] Im {Y(2,1)}

[3] Y(2,0)

[4] Re {Y(2,1)}

[5] Re {Y(2,2)}

[6] Im {Y(4,4)}

[7] Im {Y(4,3)}

etc...

syntax:     csdeconv [ options ] dwi response SH

Arguments

dwi the input diffusion-weighted image.
response the diffusion-weighted signal response function for a single fibre population.
SH the output spherical harmonics coefficients image.

Options

-grad encoding specify the diffusion-weighted gradient scheme used in the acquisition. The program will normally attempt to use the encoding stored in image header.
encoding the gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2).
-lmax order set the maximum harmonic order for the output series. By default, the program will use the highest possible lmax given the number of diffusion-weighted images.
order the maximum harmonic order to use.
-mask image only perform computation within the specified binary brain mask image.
image the mask image to use.
-directions file specify the directions over which to apply the non-negativity constraint (by default, the built-in 300 direction set is used
file a text file containing the [ el az ] pairs for the directions.
-filter spec the linear frequency filtering parameters used for the initial linear spherical deconvolution step (default = [ 1 1 1 0 0 ]).
spec a text file containing the filtering coefficients for each even harmonic order.
-normalise normalise the DW signal to the b=0 image
-lambda value the regularisation parameter lambda that controls the strength of the constraint (default = 1.0).
value the value of lambda to use.
-threshold value the threshold below which the amplitude of the FOD is assumed to be zero, expressed as a fraction of the mean value of the initial FOD (default = 0.1).
value the value of lambda to use.
-niter number the maximum number of iterations to perform for each voxel (default = 50).
number the maximum number of iterations to use.
-info display information messages.
-quiet do not display information messages or progress status.
-debug display debugging messages.
-help display this information page and exit.
-version display version information and exit.

Donald Tournier
MRtrix version 0.2.12
Last updated 2013-10-07