shconv

Synopsis

Perform spherical convolution

Usage

shconv [ options ]  odf response [ odf response ... ] SH_out
  • odf response: pairs of input ODF image and corresponding responses
  • SH_out: the output spherical harmonics coefficients image.

Description

Provided with matching pairs of response function and ODF images (containing SH coefficients), perform spherical convolution to provide the corresponding SH coefficients of the signal.

If multiple pairs of inputs are provided, their contributions will be summed into a single output.

If the responses are multi-shell (with one line of coefficients per shell), the output will be a 5-dimensional image, with the SH coefficients of the signal in each shell stored at different indices along the 5th dimension.

The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link:
https://mrtrix.readthedocs.io/en/3.0_RC4/concepts/spherical_harmonics.html

The spherical harmonic coefficients are stored according the conventions described the main documentation, which can be found at the following link:
https://mrtrix.readthedocs.io/en/3.0_RC4/concepts/spherical_harmonics.html

Options

Data type options

  • -datatype spec specify output image data type. Valid choices are: float32, float32le, float32be, float64, float64le, float64be, int64, uint64, int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le, int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be, cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be, int8, uint8, bit.

Stride options

  • -strides spec specify the strides of the output data in memory; either as a comma-separated list of (signed) integers, or as a template image from which the strides shall be extracted and used. The actual strides produced will depend on whether the output image format can support it.

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

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: David Raffelt (david.raffelt@florey.edu.au) and J-Donald Tournier (jdtournier@gmail.com)

Copyright: Copyright (c) 2008-2019 the MRtrix3 contributors.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

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