# transformcalc¶

## Synopsis¶

Perform calculations on linear transformation matrices

## Usage¶

transformcalc [ options ]  inputs [ inputs ... ] operation output

• inputs: the input(s) for the specified operation
• operation: the operation to perform, one of: invert, half, rigid, header, average, interpolate, decompose, align_vertices_rigid, align_vertices_rigid_scale (see description section for details).
• output: the output transformation matrix.

## Example usages¶

• Invert a transformation:

$transformcalc matrix_in.txt invert matrix_out.txt  • Calculate the matrix square root of the input transformation (halfway transformation): $ transformcalc matrix_in.txt half matrix_out.txt

• Calculate the rigid component of an affine input transformation:

$transformcalc affine_in.txt rigid rigid_out.txt  • Calculate the transformation matrix from an original image and an image with modified header: $ transformcalc mov mapmovhdr header output

• Calculate the average affine matrix of a set of input matrices:

$transformcalc input1.txt ... inputN.txt average matrix_out.txt  • Create interpolated transformation matrix between two inputs: $ transformcalc input1.txt input2.txt interpolate matrix_out.txt


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

• Decompose transformation matrix M into translation, rotation and stretch and shear (M = T * R * S):

transformcalc matrix_in.txt decompose matrixes_out.txt  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 • Calculate transformation that aligns two images based on sets of corresponding landmarks:  transformcalc input moving.txt fixed.txt align_vertices_rigid rigid.txt


Similary, ‘align_vertices_rigid_scale’ produces an affine matrix (rigid and global scale). 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

## Options¶

### 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).