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.
Beta feature
CLI Bulk Ingest is currently in beta. This feature is designed to improve performance and stability when importing large volumes of historical data. CLI Bulk Ingest requires an upgrade to our new V3 infrastructure, which we will begin deploying to sites starting in April 2020.
We do not recommend using Bulk Ingest until your site is upgraded to V3 because this infrastructure change is required to the improved upload performance. If your site is on V2 infrastructure, continue to use the import command to upload historical data. Contact your site admin to see which version your site is on.
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Required argument |
Description |
|---|---|
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SRC |
The path to the DICOM data you wish to import |
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GROUP_ID |
Enter an existing Flywheel group id or create a new group id |
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PROJECT_LABEL |
Enter an existing Flywheel project label or create a new project |
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.
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Optional arguments |
Description |
|---|---|
|
-h, --help |
show this help message and exit |
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--subject LABEL |
Override value for the subject label (default: None) |
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--session LABEL |
Override value for the session label (default: None) |
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-v, --verbose |
Get more detailed output (default:False) |
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-y, --yes |
Assume the answer is yes to all prompts (default:False) |
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--symlinks |
Follow symbolic links that resolve to directories (default: False) |
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--include-dirs PATTERN |
Patterns of directories to include (default: []) NoteWhen S3 bucket is configured as source, this flag does not support regex wildcard match, only “starts with.”
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--exclude-dirs PATTERN |
Patterns of directories to exclude (default: []) |
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--include PATTERN |
Patterns of filenames to include (default: []) |
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--exclude PATTERN |
Patterns of filenames to exclude (default: []) |
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--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 |
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--ignore-unknown-tags |
Ignore unknown dicom tags when parsing dicom files (default: False) |
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--encodings ENCODINGS |
Set character encoding aliases. E.g. win_1251=cp1251 (default: []) |
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--de-identify |
De-identify DICOM files (default: False) |
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--deid-profile NAME |
Use the De-identify profile by name (default: minimal) |
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--skip-existing |
Skip import of existing files (default: False) |
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--no-audit-log |
Skip uploading audit log to the target projects (default: False) |
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--load-subjects PATH |
Load subjects from the specified file (default: None) |
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--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 |
These config options are only available when using cluster mode with the “--follow” argument or when using local worker.
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Optional argument |
Description |
|---|---|
|
--save-audit-log PATH |
Save audit log to the specified path on the current machine (default: None) |
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--save-deid-log PATH |
Save de-id log to the specified path on the current machine (default: None) |
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--save-subjects PATH--save-subjects PATH |
Save subjects to the specified file (default: None) |
These config options apply when using a cluster to ingest data. The cluster
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Optional argument |
Description |
|---|---|
|
--cluster CLUSTER |
Ingest cluster url (default: None) |
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-f, --follow |
Follow the progress of the ingest (default: False) |
These config options are only available when using local worker (--cluster is not defined)
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Optional argument |
Description |
|---|---|
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--jobs JOBS |
The number of concurrent jobs to run (e.g. scan jobs), ignored when using cluster (default: 4) |
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--sleep-time SECONDS |
Number of seconds to wait before trying to get a task (default: 1) |
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--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) |
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Optional argument |
Description |
|---|---|
|
-C PATH, --config-file |
Specify configuration options via config file. Learn more about how to create this file. |
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--no-config |
Do NOT load the default configuration file |
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-y, --yes |
Assume the answer is yes to all prompts |
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--ca-certs CA_CERTS |
Set the effective local timezone for imports |
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--timezone TIMEZONE |
Set the effective local timezone for imports |
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-q, --quiet |
Squelch log messages to the console |
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-d, --debug |
Turn on debug logging |
|
-v, --verbose |
Get more detailed output |
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