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]
                [-J N_JOBS] [--seed SEED] [--output-dir OUTPUT_DIR]
                [--write-hdf5] [--gradient-file FILE [FILE ...]]
                [--b0-file FILE] [--ignore-b0] [--timing-file FILE]
                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, --omp-nthreads, --ncpus

Maximum number of threads an individual process may use.

-J, --n-jobs, --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.

Options for dMRI inputs

--gradient-file

A gradient file containing b-vectors and b-values

--b0-file

A NIfTI file containing the b-zero reference

--ignore-b0

Ignore the low-b reference and use the robust signal maximum

Options for PET inputs

--timing-file

A NIfTI file containing the timing information (onsets and durations) corresponding to the input file