usage: dipy_apply_transform [-h] [–transform_type str] [–out_dir str]

[–out_file str] static_image_files moving_image_files transform_map_file

positional arguments:

static_image_files Path of the static image file. moving_image_files Path of the moving image(s). It can be a single image or a folder containing multiple images. transform_map_file For the affine case, it should be a text(*.txt) file containing the affine matrix. For the diffeomorphic case, it should be a nifti file containing the mapping displacement field in each voxel with this shape (x, y, z, 3, 2)

optional arguments:
-h, --help

show this help message and exit

--transform_type str

Select the transformation type to apply between ‘affine’ or ‘diffeomorphic’. (default affine)

output arguments(optional):
--out_dir str

Directory to save the transformed files (default ‘’).

--out_file str

Name of the transformed file (default ‘transformed.nii.gz’). It is recommended to use the flag –mix-names to prevent the output files from being overwritten.

References: Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.