CLI command reference: Ingest dicom

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

-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:

--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:

--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-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:

--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 ignore with this cli option.

Flywheel uses the pydicom dictionary to determine known tags

--include PATTERN

Patterns of filenames to include (default: [])

For example:

--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:

--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)

-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

--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 CLUSTER

Ingest cluster url (default: None)

-f, --follow

Follow the progress of the ingest (default: False)

--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)