CLI command reference: Ingest dicom

  • Updated

Theingest 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 [SRC] [group id] [project label] [optional arguments]

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

Optional arguments

Tip

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

Optional arguments

Description

-h, --help

show this help message and exit

--subject LABEL

Override value for the subject label (default: None)

--session LABEL    

Override value for the session label (default: None)

-v, --verbose

Get more detailed output (default:False)

-y, --yes

Assume the answer is yes to all prompts (default:False)

--symlinks

Follow symbolic links that resolve to directories                       

 (default: False)

--include-dirs PATTERN

Patterns of directories to include (default: [])

Note

When S3 bucket is configured as source, this flag does not support regex wildcard match, only “starts with.”

Include-dirs: OHM/101-10

Will match:OHM/101-105, OHM/101-106, etc

--exclude-dirs PATTERN

Patterns of directories to exclude (default: [])

--include PATTERN

Patterns of filenames to include (default: [])

--exclude PATTERN

Patterns of filenames to exclude (default: [])

--compression-level COMPRESSION_LEVEL

The compression level to use for packfiles -1 by default. 0 for store. A higher compression level number means more compression

--ignore-unknown-tags

Ignore unknown dicom tags when parsing dicom files (default: False)

--encodings ENCODINGS

Set character encoding aliases. E.g. win_1251=cp1251  (default: [])

--de-identify

De-identify DICOM files (default: False)

--deid-profile NAME

Use the De-identify profile by name (default: minimal)

--skip-existing

Skip import of existing files (default: False)

--no-audit-log

Skip uploading audit log to the target projects  (default: False)

--load-subjects PATH

Load subjects from the specified file (default: None)

--detect-duplicates

Identify duplicate data conflicts within source data and duplicates between source data and data in Flywheel. Duplicates are skipped and noted in audit log. 

In the audit log the error categories are:

- `DD01` multiple files have the same destination path
- `DD02` file name already exists in destination container
- `DD03` a single item contains multiple StudyInstanceUIDs
- `DD04` a single session contains multiple StudyInstanceUIDs
- `DD05` multiple sessions have the same StudyInstanceUID
- `DD06` StudyInstanceUID already exists in a different session
- `DD07` a single acquisition contains multiple SeriesInstanceUIDs
- `DD08` multiple acquisitions have the same SeriesInstanceUID
- `DD09` a single item contains multiple SeriesInstanceUIDs
- `DD10` SeriesInstanceUID already exists in a different acquisition
- `DD11` SOPInstanceUID occurs multiple times (image uids should be unique)

--require-project

Proceed with the ingest process only if the resolved
group and project exists (default: False)

Note

A new group/project will be created if the resolved group/project do not exist and this command is not invoked. 

--enable-project-files

Enable file uploads to project container (default:
False)

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 URL

Recruits resources from the cluster your V3 Flywheel site is installed on. Use when uploading a large amount of data.

Your cluster URL is the URL you use to sign in followed by /ingest. For example: https://university.flywheel.io/cluster

-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)

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