omni_realign4d#

Overview#

omni_realign4d

bids_sidecar: A BIDS sidecar .json file containing metadata related to the EPI image.

-r REF_IDX, --ref_idx REF_IDX: Index of reference to use for SpaceTimeRealign.

-l LOOPS ..., --loops LOOPS ... (Number of Arguments: ∞) (default: [1, 1, 1]): The LOOPS parameter is a list of integers (the same size as the list of integers used for the --subsample parameter) that dictates the number of refining iterations at the corresponding subsampling resolution.

-s SUBSAMPLE ..., --subsample SUBSAMPLE ... (Number of Arguments: ∞) (default: [5, 3, 1]): SUBSAMPLE is a list of integers (at least one value) describing the subsampling sequence used when performing simultaneous slice time and motion correction. The number of elements in this list of integers must match the number of integers used for the -l or --loops parameters.

--config_file CONFIG_FILE: A TOML config file that specifies the arguments to use for this program. This provides an alternative way to specify arguments to the program. Note that this file follows the TOML standard: https://toml.io/en/. Arguments set for a particular program should follow under a table heading with the name of the program (e.g. [omni_realign4d]). Alternatively, arguments for multiple programs can be set using the [Global] table heading. To generate a config file for this program see the --generate_config option. Note that arguments in the config are loaded in BEFORE arguments specified on the command-line. This means when the same argument is specified in both the command line and the config file, the program will use the argument value specified on the command-line. In addition, if the same argument is provided in the [Global] and [omni_realign4d] tables, the argument under [omni_realign4d] takes precedence.

--generate_config GENERATE_CONFIG: Path to a location (with .toml extension) to write a config file for this program. This will generate a TOML file with all options set to their current values.

-n NUMBER_OF_THREADS, --number_of_threads NUMBER_OF_THREADS (default: 8): An integer number representing the number of of threads to use for OpenMP, OpenBLAS, and ITK based components of the program. Generally a larger number is better if you can manage it, but past 16 or so there may be diminishing returns.