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).
- -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¶
- -shells b-values specify one or more b-values to use during processing, as a comma-separated list of the desired approximate b-values (b-values are clustered to allow for small deviations). Note that some commands are incompatible with multiple b-values, and will report an error if more than one b-value is provided. WARNING: note that, even though the b=0 volumes are never referred to as shells in the literature, they still have to be explicitly included in the list of b-values as provided to the -shell option! Several algorithms which include the b=0 volumes in their computations may otherwise return an undesired result.
- -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; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
- -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).
- -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
- -help display this information page and exit.
- -version display version information and exit.
Smith, R. E.; Dhollander, T. & Connelly, A. Constrained linear least squares estimation of anisotropic response function for spherical deconvolution. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 23.
Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137
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