Index Symbols | B | C | D | F | G | L | M | P | Q | R | S | T | U | W Symbols --basedir command line option --container_specific_config command line option --creat_bids_config command line option --lc_config command line option --name command line option --output command line option --output_dir command line option --quiet command line option --run_lc command line option --sub_ses_list command line option, [1] --workdir command line option, [1] -b command line option -cbc command line option -cc command line option -lcc command line option -n command line option -o command line option, [1] -q command line option -R command line option -ssl command line option, [1] -w command line option, [1] B backup_old_rtp2pipeline_log() (in module launchcontainers.check.check_dwi_pipelines) batch_rsync_tracts() (in module launchcontainers.quality_control.batch_sync_tract_and_mrtrix) C check_all_sub() (in module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline) check_and_tract_dir() (in module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline) check_and_unzip_tract_wrapper() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) check_dwi_analysis_folder() (in module launchcontainers.check.check_dwi_pipelines) check_rtp_preproc_logs() (in module launchcontainers.quality_control.qc_rtp2preproc_output) check_subses_output() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) check_symlink() (in module launchcontainers.utils) check_tract_completeness() (in module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline) check_tractparam() (in module launchcontainers.check.check_dwi_pipelines) cli_show_folder_struc() (in module launchcontainers.check.general_checks) command line option --basedir --container_specific_config --creat_bids_config --lc_config --name --output --output_dir --quiet --run_lc --sub_ses_list, [1] --workdir, [1] -b -cbc -cc -lcc -n -o, [1] -q -R -ssl, [1] -w, [1] copy_configs() (in module launchcontainers.utils) copy_example_configs() (in module launchcontainers.helper_function.copy_configs) copy_file() (in module launchcontainers.utils) D die() (in module launchcontainers.utils) do_zip_configs() (in module launchcontainers.helper_function.zip_example_config) F find_newest_log() (in module launchcontainers.quality_control.qc_rtp2preproc_output) find_subseslist() (in module launchcontainers.quality_control.batch_sync_tract_and_mrtrix) (in module launchcontainers.quality_control.continue_run_rtp2pipeline) (in module launchcontainers.quality_control.qc_rtp2preproc_output) (in module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline) (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) flatten_directory() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) force_symlink() (in module launchcontainers.utils) G gen_cmd_prefix() (in module launchcontainers.gen_jobscript.gen_container_cmd) gen_launch_cmd() (in module launchcontainers.gen_jobscript) gen_matlab_cmd() (in module launchcontainers.gen_jobscript.gen_matlab_cmd) gen_py_cmd() (in module launchcontainers.gen_jobscript.gen_py_cmd) gen_RTP2_cmd() (in module launchcontainers.gen_jobscript.gen_container_cmd) gen_sge_array_job_script() (in module launchcontainers.clusters.sge) gen_slurm_array_job_script() (in module launchcontainers.clusters.slurm) gen_subseslist() (in module launchcontainers.helper_function.gen_subses) get_expected_tract_files() (in module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline) get_git_root() (in module launchcontainers.helper_function.zip_example_config) L launch_jobs() (in module launchcontainers.do_launch) launch_parallel() (in module launchcontainers.clusters.local) launch_serial() (in module launchcontainers.clusters.local) launchcontainers.check.check_dwi_pipelines module launchcontainers.check.general_checks module launchcontainers.cli module launchcontainers.clusters.local module launchcontainers.clusters.sge module launchcontainers.clusters.slurm module launchcontainers.do_launch module launchcontainers.do_prepare module launchcontainers.do_qc module launchcontainers.gen_jobscript module launchcontainers.gen_jobscript.gen_container_cmd module launchcontainers.gen_jobscript.gen_matlab_cmd module launchcontainers.gen_jobscript.gen_py_cmd module launchcontainers.helper_function.copy_configs module launchcontainers.helper_function.create_bids module launchcontainers.helper_function.gen_subses module launchcontainers.helper_function.zip_example_config module launchcontainers.log_setup module launchcontainers.quality_control.batch_sync_tract_and_mrtrix module launchcontainers.quality_control.continue_run_rtp2pipeline module launchcontainers.quality_control.qc_rtp2preproc_output module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline module launchcontainers.quality_control.rtp2pipelne_unzip_output module launchcontainers.utils module load_tract_params() (in module launchcontainers.quality_control.qc_tract_finish_rtp2pipeline) log_critical() (in module launchcontainers.log_setup) log_debug() (in module launchcontainers.log_setup) log_error() (in module launchcontainers.log_setup) log_info() (in module launchcontainers.log_setup) log_warning() (in module launchcontainers.log_setup) M main() (in module launchcontainers.cli) (in module launchcontainers.do_launch) (in module launchcontainers.do_prepare) (in module launchcontainers.do_qc) (in module launchcontainers.helper_function.copy_configs) (in module launchcontainers.helper_function.create_bids) (in module launchcontainers.helper_function.gen_subses) (in module launchcontainers.quality_control.continue_run_rtp2pipeline) module launchcontainers.check.check_dwi_pipelines launchcontainers.check.general_checks launchcontainers.cli launchcontainers.clusters.local launchcontainers.clusters.sge launchcontainers.clusters.slurm launchcontainers.do_launch launchcontainers.do_prepare launchcontainers.do_qc launchcontainers.gen_jobscript launchcontainers.gen_jobscript.gen_container_cmd launchcontainers.gen_jobscript.gen_matlab_cmd launchcontainers.gen_jobscript.gen_py_cmd launchcontainers.helper_function.copy_configs launchcontainers.helper_function.create_bids launchcontainers.helper_function.gen_subses launchcontainers.helper_function.zip_example_config launchcontainers.log_setup launchcontainers.quality_control.batch_sync_tract_and_mrtrix launchcontainers.quality_control.continue_run_rtp2pipeline launchcontainers.quality_control.qc_rtp2preproc_output launchcontainers.quality_control.qc_tract_finish_rtp2pipeline launchcontainers.quality_control.rtp2pipelne_unzip_output launchcontainers.utils P parse_hms() (in module launchcontainers.utils) prepare() (in module launchcontainers.cli) print_option_for_review() (in module launchcontainers.check.general_checks) process_single_subject() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) process_tracts() (in module launchcontainers.quality_control.continue_run_rtp2pipeline) Q qc() (in module launchcontainers.cli) (in module launchcontainers.do_qc) R read_df() (in module launchcontainers.utils) read_yaml() (in module launchcontainers.utils) rsync_single_subject() (in module launchcontainers.quality_control.batch_sync_tract_and_mrtrix) run() (in module launchcontainers.cli) S save_processing_summary() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) set_log_files() (in module launchcontainers.log_setup) setup_verbosity() (in module launchcontainers.log_setup) T times_match() (in module launchcontainers.utils) U unzip_subses_output() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) unzipping_tracts_parallel() (in module launchcontainers.quality_control.rtp2pipelne_unzip_output) W write_job_script() (in module launchcontainers.do_launch)