m2m_compute_transform_matrix

Compute an Affine transformation matrix for a specific resolution in the Allen using ANTsPyX.

Thoses matrices are needed for the other scripts in order to align Allen data on User Data Space.
>>> m2m_compute_transform_matrix.py path/to/reference.nii.gz
    path/to/matrix.mat resolution

usage: m2m_compute_transform_matrix.py [-h] [-c] [-f]
                                       reference out_mat {10,25,50,100}
                                       user_res

Positional Arguments

reference

Path to reference volume (.nii.gz)

out_mat

Path to output matrix (.mat)

res

Possible choices: 10, 25, 50, 100

Resolution (in micron) of the Allen files Please use the same resolution as the transformation matrix.

user_res

Reference resolution, in micron.

Named Arguments

-c, --nocache

Update the Allen Mouse Brain Connectivity Cache

Default: False

-f

Force overwriting of the output files.

Default: False

Author : Mahdi