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CLI Command Reference: Ingest Dicom

Introduction

The ingest dicom command reads through directories of DICOM files and uses the DICOM header information to group them into the correct Acquisitions and Sessions in Flywheel. The ingest dicom command requires Flywheel CLI version 11.0 or later.

This article explains the optional arguments for the import dicom command. See this article for directions on how to run the ingest dicom command.

Usage

fw ingest dicom [path to dicom data] [group id] [project label] [optional arguments]

Instruction Steps

Required Arguments

Required argument	Description
SRC	The path to the DICOM data you wish to import
GROUP_ID	Enter an existing Flywheel group id or create a new group id
PROJECT_LABEL	Enter an existing Flywheel project label or create a new project

By default, Flywheel uses the following DICOM tags to label data. If your scans are missing these tags, the --subject and --session flags are also required to successfully upload your data.


Required DICOM tag	Flywheel label	CLI flag to use if missing
`PatientID`	Subject label	`--subject <subjectLabel>`
`StudyDescription`	Session label	`--session <sessionLabel>`

If your scans do have values for the PatientID and StudyDescription fields, you do not need to use these flags. However, you can use them to change the default labels for the subjects and sessions.

fw ingest dicom ~/Documents/MyData/Study001 mygroup "A project"   
--subject 01 --session 01

Optional Arguments

If you are using multiple optional arguments in your command, consider creating a config file. See the article for more information on creating and using a config file.

Optional arguments	Description
-h, --help	show this help message and exit
--compression-level	The compression level to use for packfiles -1 by default. 0 for store. A higher compression level number means more compression
--copy-duplicates	Upload duplicate files to a new project when using `--detect-duplicates` The project created for the duplicates will be named [target project label] _TimestampOfIngest. The duplicates project will have the same permissions as the original destination project. No additional project artifacts need to be copied (gear rules, data views, description, etc).
--de-identify	De-identify DICOM files, e-files and p-files prior to upload. Applies custom de-identification when used with a deid-profile set in a configuration file. By default, it will apply the minimal de-identification to DICOM files: * Remove Patient ID, Patient Name, and Patient Birthdate * Patient Age convert to months
--de-id profile NAME	Use the De-identify profile by name. Use this flag if you have multiple de-id profiles in a single config.
--detect-duplicates	Flywheel scans both the source dataset and any data already in the Flywheel project. Flywheel looks for the following: * File path conflict in the source dataset- File path in the upload dataset is not unique File path conflict in Flywheel - file already exists Duplicate `StudyInstanceUID` in source dataset Duplicate `StudyInstanceUID` in Flywheel - UID already exists Duplicate `SeriesInstanceUID` in the source dataset Duplicate `SeriesInstanceUID` in Flywheel - UID already exists Duplicate `SOPInstanceUID` in series
--detect-duplicates-project DETECT_DUPLICATES_PROJECT	Specify one or multiple project paths to use for detecting duplicates
--enable-project-files	Enable file uploads to a project container
--encodings ENCODINGS	Set character encoding aliases. E.g. win_1251=cp1251
--exclude PATTERN	Patterns of filenames to exclude. For example: * Exclude a single file: `--exclude="ReadMe.md"` * Exclude all files of a specific filetype `--exlcude="*.md"`
--exclude-dirs PATTERN	Patterns of directories to exclude (default: []) For example:`--exclude-dirs="Sub-01"` excludes all files and folder within the Sub-01 folder. This means the following directories would not be uploaded: * Sub-01/Sess01 * Sub-01/Sess2/Acq02
--force-scan	Try to parse all files as DICOM files regardless of the DICM prefix. (default: False) (might want to use `--include "\*"`)
-g ID, --group ID	The id of the group if not in the folder structure
--group-override ID	Force using this group id
--ignore-unknown-tags	Ignore unknown dicom tags when parsing dicom files (default: False) By default ingest can fail if the tag is not private and has implicit VR and not in this list. These tags can be ignored with this cli option. Flywheel uses the pydicom dictionary to determine known tags
--include PATTERN	Patterns of filenames to include (default: []) For example: * Include a single file: `--include="participants.csv"` * Include all files of a filetype: `--include="*.dcm"`
--include-dirs PATTERN	Patterns of directories to include (default: []) `--incude-dirs="OHM/101-10\"` The regex wildcard means that this would include the directories like: OHM/101-105* OHM/101-106 * OHM/101-1011 Note: When S3 bucket is configured as source, this flag does not support regex wildcard match, only “starts with.”
--load-subject PATH	Load subjects from the specified file
--no-audit-log	Skip uploading audit log to the target projects
--require-project	Proceed with the ingest process only if the resolved group and project exists (default: False) By default, Flywheel creates a new group or project if an existing group ID or project label does not match what you designated in your command or template. This means if you mistype the group id or project label, your data will be uploaded in the wrong location. Use this flag to make sure your data is only uploaded to existing groups and projects.
--session LABEL	Override value for the session label
--skip-existing	Looks at filenames for files already in your project, and skip import of files with the same filename. (default: False)
--subject LABEL	Override value for the subject label
--symlinks	Follow symbolic links that resolve to directories (default: False)

General

Optional argument	Description
-C PATH, --config-file	Specify configuration options via config file. Learn more about how to create this file.
--no-config	Do NOT load the default configuration file
-y, --yes	Assume the answer is yes to all prompts
--ca-certs CA_CERTS	Set the effective local timezone for imports
--timezone TIMEZONE	Set the effective local timezone for imports
-q, --quiet	Squelch log messages to the console
-d, --debug	Turn on debug logging
-v, --verbose	Get more detailed output

Reporter

These config options are only available when using cluster mode with the “--follow” argument or when using local worker.

Optional argument	Description
--save-audit-log PATH	Save audit log to the specified path on the current machine (default: None)
--save-deid-log PATH	Save de-id log to the specified path on the current machine (default: None)
--save-subjects PATH--save-subjects PATH	Save subjects to the specified file (default: None)

Cluster Config

These config options apply when using a cluster to ingest data. The cluster

Optional argument	Description
--cluster CLUSTER	Ingest cluster url (default: None)
-f, --follow	Follow the progress of the ingest (default: False)

Worker Config

These config options are only available when using local worker (--cluster is not defined)

Optional argument	Description
--jobs JOBS	The number of concurrent jobs to run (e.g. scan jobs), ignored when using cluster (default: 4)
--sleep-time SECONDS	Number of seconds to wait before trying to get a task (default: 1)
--max-tempfile MAX_TEMPFILE	The max in-memory tempfile size, in MB, or 0 to always use disk (default: 50)The max in-memory tempfile size, in MB, or 0 to always use disk (default: 50)