Running NiFreeze

Command line interface

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

usage: nifreeze [-h] [--brainmask BRAINMASK] [--align-config ALIGN_CONFIG]
                [--models MODELS [MODELS ...]] [--nthreads NTHREADS]
                [--njobs NJOBS] [--seed SEED] [--output-dir OUTPUT_DIR]
                [--write-hdf5]
                input_file

Positional Arguments

input_file

Path to the HDF5 file containing the original 4D data.

Named Arguments

--brainmask

Path to a brain mask in NIfTI format.

--align-config

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

--models

Select the data model to generate 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.

--write-hdf5

Generate an HDF5 file also.