.. _amp2response:

amp2response
===================

Synopsis
--------

Estimate response function coefficients based on the DWI signal in single-fibre voxels

Usage
--------

::

    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

Description
-----------

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).

Options
-------

-  **-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.  |br|
   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)

Standard options
^^^^^^^^^^^^^^^^

-  **-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.

References
^^^^^^^^^^

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

--------------



**Author:** Robert E. Smith (robert.smith@florey.edu.au) and J-Donald Tournier (jdtournier@gmail.com)

**Copyright:** Copyright (c) 2008-2021 the MRtrix3 contributors.

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License, v. 2.0. If a copy of the MPL was not distributed with this
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Covered Software is provided under this License on an "as is"
basis, without warranty of any kind, either expressed, implied, or
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See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.


