Estimate response function coefficients based on the DWI signal in single-fibre voxels
amp2response [ options ] amps mask directions response
- amps: the amplitudes image
- mask: the mask containing the voxels from which to estimate the response function
- directions: a 4D image containing the estimated fibre directions
- response: the output zonal spherical harmonic coefficients
This command uses the image data from all selected single-fibre voxels concurrently, rather than simply averaging their individual spherical harmonic coefficients. It also ensures that the response function is non-negative, and monotonic (i.e. its amplitude must increase from the fibre direction out to the orthogonal plane).
If multi-shell data are provided, and one or more b-value shells are not explicitly requested, the command will generate a response function for every b-value shell (including b=0 if present).
For details on the method provided by this command see: https://www.researchgate.net/publication/307862932_Constrained_linear_least_squares_estimation_of_anisotropic_response_function_for_spherical_deconvolution
- -isotropic estimate an isotropic response function (lmax=0 for all shells)
- -noconstraint disable the non-negativity and monotonicity constraints
- -directions path provide an external text file containing the directions along which the amplitudes are sampled
DW Shell selection options¶
- -shell list specify one or more diffusion-weighted gradient shells to use during processing, as a comma-separated list of the desired approximate b-values. Note that some commands are incompatible with multiple shells, and will throw an error if more than one b-value is provided.
- -lmax values specify the maximum harmonic degree of the response function to estimate (can be a comma-separated list for multi-shell data)
- -info display information messages.
- -quiet do not display information messages or progress status.
- -debug display debugging messages.
- -force force overwrite of output files. Caution: Using the same file as input and output might cause unexpected behaviour.
- -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading)
- -failonwarn terminate program if a warning is produced
- -help display this information page and exit.
- -version display version information and exit.
Author: Robert E. Smith (firstname.lastname@example.org)
Copyright: Copyright (c) 2008-2017 the MRtrix3 contributors.
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