diff --git a/boutiques_descriptors/dcm2bids_3_2.json b/boutiques_descriptors/dcm2bids_3_2.json new file mode 100644 index 0000000..e56fc94 --- /dev/null +++ b/boutiques_descriptors/dcm2bids_3_2.json @@ -0,0 +1,147 @@ +{ + "description": "DICOM to BIDS converter", + "command-line": "dcm2bids [DICOM_DIR] [PARTICIPANT] [SESSION] [CONFIG] [OUTPUT_DIR] [AUTO_EXTRACT_ENTITIES] [DO_NOT_REORDER_ENTITIES] [BIDS_VALIDATE] [FORCE_DCM2BIDS] [SKIP_DCM2NIIX] [CLOBBER] [LOG_LEVEL] [VERSION]", + "tags": { + "domain": [ + "nifti", + "bids", + "neuro-imaging" + ] + }, + "tool-version": "3.2.0", + "inputs": [ + { + "description": "DICOM directory(ies) or archive(s) (tar, tar.bz2, tar.gz or zip).", + "name": "dicom_dir", + "command-line-flag": "-d", + "optional": false, + "list": true, + "type": "String", + "id": "dicom_dir", + "value-key": "[DICOM_DIR]" + }, + { + "description": "Participant ID", + "name": "participant", + "command-line-flag": "-p", + "optional": false, + "type": "String", + "id": "participant", + "value-key": "[PARTICIPANT]" + }, + { + "description": "Session ID", + "name": "session", + "command-line-flag": "-s", + "optional": true, + "type": "String", + "id": "session", + "value-key": "[SESSION]" + }, + { + "description": "JSON configuration file (see manual online https://unfmontreal.github.io/Dcm2Bids/3.2.0/how-to/create-config-file/ ", + "name": "config", + "command-line-flag": "-c", + "optional": false, + "type": "String", + "id": "config", + "value-key": "[CONFIG]" + }, + { + "description": "Output BIDS directory. [%(default)s]", + "name": "output_dir", + "command-line-flag": "-o", + "optional": true, + "type": "String", + "id": "output_dir", + "value-key": "[OUTPUT_DIR]" + }, + { + "description": "If set, it will automatically try to extract entity information [task, dir, echo] based on the suffix and datatype. ", + "name": "auto_extract_entities", + "command-line-flag": "--auto_extract_entities", + "optional": true, + "type": "Flag", + "id": "auto_extract_entities", + "value-key": "[AUTO_EXTRACT_ENTITIES]" + }, + { + "description": "If set, it will not reorder entities according to the relative ordering indicated in the BIDS specification and use the order defined in custom_entities by the user.\nCannot be used with --auto_extract_entities. [%(default)s]", + "name": "do_not_reorder_entities", + "command-line-flag": "--do_not_reorder_entities", + "optional": true, + "type": "Flag", + "id": "do_not_reorder_entities", + "value-key": "[DO_NOT_REORDER_ENTITIES]" + }, + { + "description": "If set, once your conversion is done it will check if your output folder is BIDS valid. [%(default)s]\nbids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart", + "name": "bids_validate", + "command-line-flag": "--bids_validate", + "optional": true, + "type": "Flag", + "id": "bids_validate", + "value-key": "[BIDS_VALIDATE]" + }, + { + "description": "Overwrite previous temporary dcm2bids output if it exists.", + "name": "force_dcm2bids", + "command-line-flag": "--force_dcm2bids", + "optional": true, + "type": "Flag", + "id": "force_dcm2bids", + "value-key": "[FORCE_DCM2BIDS]" + }, + { + "description": "Skip dcm2niix conversion. Option -d should contains NIFTI and json files.", + "name": "skip_dcm2niix", + "command-line-flag": "--skip_dcm2niix", + "optional": true, + "type": "Flag", + "id": "skip_dcm2niix", + "value-key": "[SKIP_DCM2NIIX]" + }, + { + "description": "Overwrite output if it exists.", + "name": "clobber", + "command-line-flag": "--clobber", + "optional": true, + "type": "Flag", + "id": "clobber", + "value-key": "[CLOBBER]" + }, + { + "default-value": "INFO", + "description": "Set logging level to the console.", + "name": "log_level", + "value-choices": [ + "DEBUG", + "INFO", + "WARNING", + "ERROR", + "CRITICAL" + ], + "optional": true, + "command-line-flag": "-l", + "type": "String", + "id": "log_level", + "value-key": "[LOG_LEVEL]" + }, + { + "description": "Report dcm2bids version and the BIDS version.", + "name": "version", + "command-line-flag": "-v", + "optional": true, + "type": "String", + "id": "version", + "value-key": "[VERSION]" + } + ], + "suggested-resources": { + "ram": 1, + "walltime-estimate": 24000, + "cpu-cores": 1 + }, + "name": "dcm2bids", + "schema-version": "0.5" +}