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