dipy_align_affine [-h] [–transform str] [–nbins int] [–sampling_prop int] [–metric str] [–level_iters [int …]] [–sigmas [float …]] [–factors [float …]]

[–progressive] [–save_metric] [–out_dir str] [–out_moved str] [–out_affine str] [–out_quality str] static_image_files moving_image_files

Positional Arguments

static_image_files Path to the static image file. moving_image_files Path to the moving image file.

Optional Arguments

-h, --help

show this help message and exit

--transform str

com: center of mass, trans: translation, rigid: rigid body, rigid_isoscaling: rigid body + isotropic scaling, rigid_scaling: rigid body + scaling, affine: full affine including translation, rotation, shearing and scaling.

--nbins int

Number of bins to discretize the joint and marginal PDF.

--sampling_prop int

Number ([0-100]) of voxels for calculating the PDF. ‘None’ implies all voxels.

--metric str

Similarity metric for gathering mutual information).

–level_iters [int …]

The number of iterations at each scale of the scale space. level_iters[0] corresponds to the coarsest scale, level_iters[-1] the finest, where n is the length of the sequence.

–sigmas [float …] Custom smoothing parameter to build the scale space (one parameter for each scale). –factors [float …]

Custom scale factors to build the scale space (one factor for each scale).


Enable/Disable the progressive registration.


If true, quality assessment metric are saved in ‘quality_metric.txt’.

Output Arguments(Optional)

--out_dir str

Directory to save the transformed image and the affine matrix (default current directory).

--out_moved str

Name for the saved transformed image.

--out_affine str

Name for the saved affine matrix.

--out_quality str

Name of the file containing the saved quality metric.


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.