SUSAN Spatial Smoothing

clpipe uses FSL’s SUSAN smoothing to perform spatial smoothing. This step is usually done after postprocessing. Options for this are configurable on a processing stream basis, see config file for more details.

Usage: susan_smoothing [OPTIONS] [SUBJECTS]...

Options:
  -config_file PATH        Use a given configuration file. If left blank, uses
                           the default config file, requiring definition of
                           BIDS, working and output directories.
  -target_dir DIRECTORY    Which directory to process. If a configuration file
                           is provided.
  -target_suffix TEXT      Which file suffix to use. If a configuration file
                           is provided with a target suffix, this argument is
                           not necessary. Defaults to "preproc_bold.nii.gz"
  -output_dir DIRECTORY    Where to put the postprocessed data. If a
                           configuration file is provided with a output
                           directory, this argument is not necessary.
  -output_suffix TEXT      What suffix to append to the smoothed files. If a
                           configuration file is provided with a output
                           suffix, this argument is not necessary.
  -task TEXT               Which task to smooth. If left blank, defaults to
                           all tasks.
  -processing_stream TEXT  Optional processing stream selector.
  -log_dir DIRECTORY       Where to put HPC output files. If not specified,
                           defaults to <outputDir>/batchOutput.
  -submit                  Flag to submit commands to the HPC.
  -batch / -single         Submit to batch, or run in current session. Mainly
                           used internally.
  -debug                   Print detailed processing information and traceback
                           for errors.
  --help                   Show this message and exit.