dipy_align_affine [-h] [–transform str] [–nbins int]

[–sampling_prop int] [–metric str] [–level_iters [int [int …]]] [–sigmas [float [float …]]] [–factors [float [float …]]] [–progressive] [–save_metric] [–out_dir str] [–out_moved str] [–out_affine str] [–out_quality str] static_img_files moving_img_files

Positional Arguments

static_img_files Path to the static image file. moving_img_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 affine: full affine including translation, rotation, shearing and scaling (default ‘affine’).

--nbins int

Number of bins to discretize the joint and marginal PDF (default ‘32’).

--sampling_prop int

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

--metric str

Similarity metric for gathering mutual information (default ‘mi’ , Mutual Information metric).

–level_iters [int [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. By default, a 3-level scale space with iterations sequence equal to [10000, 1000, 100] will be used.

–sigmas [float [float …]]

Custom smoothing parameter to build the scale space (one parameter for each scale). By default, the sequence of sigmas will be [3, 1, 0].

–factors [float [float …]]

Custom scale factors to build the scale space (one factor for each scale). By default, the sequence of factors will be [4, 2, 1].


Enable/Disable the progressive registration (default ‘True’).


If true, quality assessment metric are saved in ‘quality_metric.txt’ (default ‘False’).

Output Arguments(Optional)

--out_dir str

Directory to save the transformed image and the affine matrix (default ‘’).

--out_moved str

Name for the saved transformed image (default ‘moved.nii.gz’).

--out_affine str

Name for the saved affine matrix (default ‘affine.txt’).

--out_quality str

Name of the file containing the saved quality metric (default ‘quality_metric.txt’).


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.