{ "name": "mriqc", "description": "mriqc", "tool-version": "23.1.0", "schema-version": "0.5", "command-line": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [VERSION] [VERBOSE_COUNT] [SPECIES] [PARTICIPANT_LABEL] [SESSION_ID] [RUN_ID] [TASK_ID] [MODALITIES] [DSNAME] [BIDS_DATABASE_DIR] [BIDS_DATABASE_WIPE] [NPROCS] [OMP_NTHREADS] [MEM] [DEBUG] [FLOAT32] [PDB] [WORK_DIR] [VERBOSE_REPORTS] [REPORTS_ONLY] [WRITE_GRAPH] [DRY_RUN] [RESOURCE_MONITOR] [USE_PLUGIN] [NO_SUB] [EMAIL] [WEBAPI_URL] [WEBAPI_PORT] [UPLOAD_STRICT] [NOTRACK] [ANTS_FLOAT] [ANTS_SETTINGS] [FFT_SPIKES_DETECTOR] [FD_THRES] [DEOBLIQUE] [DESPIKE] [START_IDX] [STOP_IDX]", "inputs": [ { "id": "bids_dir", "name": "bids_dir", "description": "The root folder of a BIDS valid dataset (sub-XXXXX folders should be found at the top level in this folder).", "optional": false, "type": "String", "value-key": "[BIDS_DIR]" }, { "id": "output_dir", "name": "output_dir", "description": "The directory where the output files should be stored. If you are running group level analysis this folder should be prepopulated with the results of the participant level analysis.", "optional": false, "type": "String", "value-key": "[OUTPUT_DIR]" }, { "id": "analysis_level", "name": "analysis_level", "description": "Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in parallel) using the same output_dir.", "optional": false, "type": "String", "value-key": "[ANALYSIS_LEVEL]", "value-choices": [ "participant", "group" ] }, { "id": "version", "name": "version", "description": "show program's version number and exit", "optional": true, "type": "Flag", "value-key": "[VERSION]", "command-line-flag": "--version" }, { "id": "verbose_count", "name": "verbose_count", "description": "Increases log verbosity for each occurrence, debug level is -vvv.", "optional": true, "type": "String", "value-key": "[VERBOSE_COUNT]", "value-choices": [ "-v", "-vv", "-vvv" ] }, { "id": "species", "name": "species", "description": "Use appropriate template for population", "optional": true, "type": "String", "value-key": "[SPECIES]", "default-value": "human", "value-choices": [ "human", "rat" ], "command-line-flag": "--species" }, { "id": "participant_label", "name": "participant_label", "description": "A space delimited list of participant identifiers or a single identifier (the sub- prefix can be removed).", "optional": true, "type": "String", "value-key": "[PARTICIPANT_LABEL]", "list": true, "command-line-flag": "--participant-label" }, { "id": "session_id", "name": "session_id", "description": "Filter input dataset by session ID.", "optional": true, "type": "String", "value-key": "[SESSION_ID]", "command-line-flag": "--session-id" }, { "id": "run_id", "name": "run_id", "description": "Filter input dataset by run ID (only integer run IDs are valid).", "optional": true, "type": "Number", "value-key": "[RUN_ID]", "command-line-flag": "--run-id" }, { "id": "task_id", "name": "task_id", "description": "Filter input dataset by task ID.", "optional": true, "type": "String", "value-key": "[TASK_ID]", "command-line-flag": "--task-id" }, { "id": "modalities", "name": "modalities", "description": "Filter input dataset by MRI type.", "optional": true, "type": "String", "value-key": "[MODALITIES]", "default-value": [ "T1w", "T2w", "bold", "dwi" ], "value-choices": [ "T1w", "T2w", "bold", "dwi" ], "command-line-flag": "-m", "list": true }, { "id": "dsname", "name": "dsname", "description": "A dataset name.", "optional": true, "type": "String", "value-key": "[DSNAME]", "command-line-flag": "--dsname" }, { "id": "bids_database_dir", "name": "bids_database_dir", "description": "Path to an existing PyBIDS database folder, for faster indexing (especially useful for large datasets).", "optional": true, "type": "String", "value-key": "[BIDS_DATABASE_DIR]", "command-line-flag": "--bids-database-dir" }, { "id": "bids_database_wipe", "name": "bids_database_wipe", "description": "Wipe out previously existing BIDS indexing caches, forcing re-indexing.", "optional": true, "type": "Flag", "value-key": "[BIDS_DATABASE_WIPE]", "command-line-flag": "--bids-database-wipe" }, { "id": "nprocs", "name": "nprocs", "description": "Maximum number of simultaneously running parallel processes executed by *MRIQC* (e.g., several instances of ANTs' registration). However, when ``--nprocs`` is greater or equal to the ``--omp-nthreads`` option, it also sets the maximum number of threads that simultaneously running processes may aggregate (meaning, with ``--nprocs 16 --omp-nthreads 8`` a maximum of two 8-CPU-threaded processes will be running at a given time). Under this mode of operation, ``--nprocs`` sets the maximum number of processors that can be assigned work within an *MRIQC* job, which includes all the processors used by currently running single- and multi-threaded processes. If ``None``, the number of CPUs available will be automatically assigned (which may not be what you want in, e.g., shared systems like a HPC cluster.", "optional": true, "type": "String", "value-key": "[NPROCS]", "command-line-flag": "--nprocs" }, { "id": "omp_nthreads", "name": "omp_nthreads", "description": "Maximum number of threads that multi-threaded processes executed by *MRIQC* (e.g., ANTs' registration) can use. If ``None``, the number of CPUs available will be automatically assigned (which may not be what you want in, e.g., shared systems like a HPC cluster.", "optional": true, "type": "String", "value-key": "[OMP_NTHREADS]", "command-line-flag": "--omp-nthreads" }, { "id": "mem", "name": "mem", "description": "Upper bound memory limit for MRIQC processes.", "optional": true, "type": "String", "value-key": "[MEM]", "command-line-flag": "--mem" }, { "id": "debug", "name": "debug", "description": "Use testing settings for a minimal footprint.", "optional": true, "type": "Flag", "value-key": "[DEBUG]", "command-line-flag": "--testing" }, { "id": "float32", "name": "float32", "description": "Cast the input data to float32 if it's represented in higher precision (saves space and improves performance).", "optional": true, "type": "Flag", "value-key": "[FLOAT32]", "default-value": true, "command-line-flag": "-f" }, { "id": "pdb", "name": "pdb", "description": "Open Python debugger (pdb) on exceptions.", "optional": true, "type": "Flag", "value-key": "[PDB]", "command-line-flag": "--pdb" }, { "id": "work_dir", "name": "work_dir", "description": "Path where intermediate results should be stored.", "optional": true, "type": "String", "value-key": "[WORK_DIR]", "command-line-flag": "-w" }, { "id": "verbose_reports", "name": "verbose_reports", "description": "No description provided.", "optional": true, "type": "Flag", "value-key": "[VERBOSE_REPORTS]", "command-line-flag": "--verbose-reports" }, { "id": "reports_only", "name": "reports_only", "description": "No description provided.", "optional": true, "type": "Flag", "value-key": "[REPORTS_ONLY]", "command-line-flag": "--reports-only" }, { "id": "write_graph", "name": "write_graph", "description": "Write workflow graph.", "optional": true, "type": "Flag", "value-key": "[WRITE_GRAPH]", "command-line-flag": "--write-graph" }, { "id": "dry_run", "name": "dry_run", "description": "Do not run the workflow.", "optional": true, "type": "Flag", "value-key": "[DRY_RUN]", "command-line-flag": "--dry-run" }, { "id": "resource_monitor", "name": "resource_monitor", "description": "Hook up the resource profiler callback to nipype.", "optional": true, "type": "Flag", "value-key": "[RESOURCE_MONITOR]", "command-line-flag": "--resource-monitor" }, { "id": "use_plugin", "name": "use_plugin", "description": "Nipype plugin configuration file.", "optional": true, "type": "String", "value-key": "[USE_PLUGIN]", "command-line-flag": "--use-plugin" }, { "id": "no_sub", "name": "no_sub", "description": "Turn off submission of anonymized quality metrics to MRIQC's metrics repository.", "optional": true, "type": "Flag", "value-key": "[NO_SUB]", "command-line-flag": "--no-sub" }, { "id": "email", "name": "email", "description": "Email address to include with quality metric submission.", "optional": true, "type": "String", "value-key": "[EMAIL]", "command-line-flag": "--email" }, { "id": "webapi_url", "name": "webapi_url", "description": "IP address where the MRIQC WebAPI is listening.", "optional": true, "type": "String", "value-key": "[WEBAPI_URL]", "command-line-flag": "--webapi-url" }, { "id": "webapi_port", "name": "webapi_port", "description": "Port where the MRIQC WebAPI is listening.", "optional": true, "type": "Number", "value-key": "[WEBAPI_PORT]", "command-line-flag": "--webapi-port" }, { "id": "upload_strict", "name": "upload_strict", "description": "Upload will fail if upload is strict.", "optional": true, "type": "Flag", "value-key": "[UPLOAD_STRICT]", "command-line-flag": "--upload-strict" }, { "id": "notrack", "name": "notrack", "description": "Opt-out of sending tracking information of this run to the NiPreps developers. This information helps to improve MRIQC and provides an indicator of real world usage crucial for obtaining funding.", "optional": true, "type": "Flag", "value-key": "[NOTRACK]", "command-line-flag": "--notrack" }, { "id": "ants_float", "name": "ants_float", "description": "Use float number precision on ANTs computations.", "optional": true, "type": "Flag", "value-key": "[ANTS_FLOAT]", "command-line-flag": "--ants-float" }, { "id": "ants_settings", "name": "ants_settings", "description": "Path to JSON file with settings for ANTs.", "optional": true, "type": "String", "value-key": "[ANTS_SETTINGS]", "command-line-flag": "--ants-settings" }, { "id": "fft_spikes_detector", "name": "fft_spikes_detector", "description": "Turn on FFT based spike detector (slow).", "optional": true, "type": "Flag", "value-key": "[FFT_SPIKES_DETECTOR]", "command-line-flag": "--fft-spikes-detector" }, { "id": "fd_thres", "name": "fd_thres", "description": "Threshold on framewise displacement estimates to detect outliers.", "optional": true, "type": "Number", "value-key": "[FD_THRES]", "default-value": 0.2, "command-line-flag": "--fd_thres" }, { "id": "deoblique", "name": "deoblique", "description": "Deoblique the functional scans during head motion correction preprocessing.", "optional": true, "type": "Flag", "value-key": "[DEOBLIQUE]", "command-line-flag": "--deoblique" }, { "id": "despike", "name": "despike", "description": "Despike the functional scans during head motion correction preprocessing.", "optional": true, "type": "Flag", "value-key": "[DESPIKE]", "command-line-flag": "--despike" }, { "id": "start_idx", "name": "start_idx", "description": "DEPRECATED Initial volume in functional timeseries that should be considered for preprocessing.", "optional": true, "type": "Number", "value-key": "[START_IDX]", "command-line-flag": "--start-idx" }, { "id": "stop_idx", "name": "stop_idx", "description": "DEPRECATED Final volume in functional timeseries that should be considered for preprocessing.", "optional": true, "type": "Number", "value-key": "[STOP_IDX]", "command-line-flag": "--stop-idx" } ], "tags": {}, "suggested-resources": { "cpu-cores": 1, "ram": 1, "walltime-estimate": 60 } }