Options

To display the options of extractor_flow, please use nextflow run extractor_flow -r 1.0.0 --help.

Optional list

--output_dir PATH (default: ./results)

Directory where to write the final results.

--run_bet BOOL (default: False)

Run bet if your t1s are not brain extracted.

--orig BOOL (default: False)

Extract all trk in diffusion space (if t1 has been provided).

--keep_intermediate_steps BOOL (default: False)

Keep intermediate steps (false). MUST be used if you need to debug.

--quick_registration BOOL (default: False)

If set, will choose antsRegistrationSyNQuick.sh instead of antsRegistrationSyN.sh.

--processes_bet_register_t1 NUMBER (default: 4)

Number of processes for T1 brain extraction task.

--processes_major_filtering NUMBER (default: 4)

Number of processes for the major filtering task (4).

--processes NUMBER (default: 4)

The number of parallel processes to launch. Only affects the local scheduler.