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.