Running NiFreeze

Command line interface

A model-based algorithm for the realignment of 4D brain images.

usage: nifreeze [-h] [--align_config ALIGN_CONFIG]
                [--models MODELS [MODELS ...]] [--nthreads NTHREADS]
                [--njobs NJOBS] [--seed SEED] [--output_dir OUTPUT_DIR]
                input_file

Positional Arguments

input_file

Path to the HDF5 file containing the original DWI data.

Named Arguments

--align_config

Path to the yaml file containing the parameters to configure the image registration process.

--models

Select the diffusion model for registration targets.

--nthreads

Maximum number of threads an individual process may use.

--njobs

Number of parallel jobs.

--seed

Seed the random number generator for deterministic estimation.

--output_dir

Path to the output directory. Defaults to the current directory.The output file will have the same name as the input file.