Perform calculations on linear transformation matrices
transformcalc [ options ] inputs [ inputs ... ] operation output
- inputs: the inputs for the specified operation
- operation: the operation to perform, one of: invert, half, rigid, header, average, interpolate, decompose, align_vertices_rigid (see description section for details).
- output: the output transformation matrix.
invert: invert the input transformation:
matrix_in invert output
half: calculate the matrix square root of the input transformation:
matrix_in half output
rigid: calculate the rigid transformation of the affine input transformation:
matrix_in rigid output
header: calculate the transformation matrix from an original image and an image with modified header:
mov mapmovhdr header output
average: calculate the average affine matrix of all input matrices:
input … average output
interpolate: create interpolated transformation matrix between input (t=0) and input2 (t=1). Based on matrix decomposition with linear interpolation of translation, rotation and stretch described in Shoemake, K., Hill, M., & Duff, T. (1992). Matrix Animation and Polar Decomposition. Matrix, 92, 258-264. doi:10.1.1.56.1336:
input input2 interpolate output
decompose: decompose transformation matrix M into translation, rotation and stretch and shear (M = T * R * S). The output is a key-value text file containing: scaling: vector of 3 scaling factors in x, y, z direction; shear: list of shear factors for xy, xz, yz axes; angles: list of Euler angles about static x, y, z axes in radians in the range [0:pi]x[-pi:pi]x[-pi:pi]; angle_axis: angle in radians and rotation axis; translation : translation vector along x, y, z axes in mm; R: composed roation matrix (R = rot_x * rot_y * rot_z); S: composed scaling and shear matrix:
matrix_in decompose output
align_vertices_rigid: align two sets of landmarks using a rigid transformation. Vertex coordinates are in scanner space, corresponding vertices must be stored in the same row of moving.txt and fixed.txt. Requires 3 or more vertices in each file. Algorithm: Kabsch ‘A solution for the best rotation to relate two sets of vectors’ DOI:10.1107/S0567739476001873:
input moving.txt fixed.txt align_vertices_rigid output
- -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).
- -help display this information page and exit.
- -version display version information and exit.
Author: Max Pietsch (email@example.com)
Copyright: Copyright (c) 2008-2018 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/
MRtrix3 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see http://www.mrtrix.org/