CLI reference guide: Import DICOM

folder

The path to the folder to import

group_id

Enter an existing group id or enter a new group_id to create the group when you import data. The group id can include lowercase letters, numbers, dashes, and underscores as long as it’s unique. It can’t be changed later.

project_label

Enter an existing project label or enter a new project label to create the group when you import data.

The project label can include lowercase letters, numbers, dashes, underscores or spaces as long as its unique. Project labels with spaces require quotes (for example "A Project Name"). The project label can be changed later.

-h

Show this help message and exit

--config-file FILE LOCATION

Specify configuration options via config file. See our article on how to create and use the config file to set optional arguments.

--no-config

Do NOT load the default configuration file

-y

Assume the answer is yes to all prompts

--ca-certs CA_CERTS

The file to use for SSL Certificate Validation

--debug

Turns on debug logging level

--quiet

Stop logging to the console

--max-retries MAX_RETRIES

Sets the maximum number of retry attempts, if assume yes. The default is 3 retry attempts.

--jobs JOBS

Allocates resources for jobs. Jobs perform tasks on your data to process and prepare it for upload to Flywheel. For example, the compression-level is a job run before the data is uploaded to Flywheel.

--concurrent-uploads CONCURRENT_UPLOADS

Allocates resources for uploading data to your Flywheel instance. The amount of concurrent uploads your computer can successfully upload depends on the amount of CPU available.

--compression-level {-1,0,1,2,3,4,5,6,7,8}

The compression level to use for packfiles. -1 for default, 0 for store. A higher compression level number means more compression (and more processing time to compress the data)

--symlinks

Follow symbolic links that resolve to directories

--include-dirs INCLUDE_DIRS

Patterns of directories to include. You can use wildcard matches (?, *) to include directories and their subdirectories.

Flywheel CLI can only import directories that are under the initial indicated directory

--exclude-dirs EXCLUDE_DIRS

Patterns of directories to exclude. You can use wildcard matches (?,*) to include directories. This does not include sub-directories.

--include FILTER

Enter specific filenames or use wildcard matches (?,*) to include patterns of filenames. You can only include files that are within the path designated in the command. Learn more about file types in Flywheel.

--exclude EXCLUDE

Enter specific filenames or use wildcard matches (?,*) to exclude patterns of filenames. Learn more about file types in Flywheel.

--output-folder OUTPUT_FOLDER

Output to the given folder instead of uploading to flywheel.

--no-uids

Ignore UIDs when grouping sessions and acquisitions. This is useful when you want to group sessions and acquisitions by labels instead of UID.

--unique-uids

Warn before creating a Flywheel container (Group, Project, Subject, Session, or Acquisition) with duplicate UIDs

--max-tempfile MAX_TEMPFILE

The max in-memory tempfile size, in MB, or 0 to always use disk

--skip-existing

Skip import of existing files.

--no-audit-log

Don't generate an audit log

--audit-log-path AUDIT_LOG_PATH

Sets the location for where the audit log should be placed.

--private-dicom-tags PRIVATE_DICOM_TAGS

Include the path to the file that defines your private DICOM tags (tags that are not standard for DICOMs and are unique to your institution).

You can then use the defined tags to de-identify the tags before uploading your data to Flywheel. See our article to learn how define and de-identify private DICOM tags.

--ignore-unknown-tags

The Flywheel CLI gives an error if there is an unknown DICOM tag. Use this flag to suppress the error and ignore unknown DICOM tags.

--encodings ENCODINGS

Set character encoding aliases. E.g. win_1251=cp1251

--related-acquisitions

Store related DICOMs in the same acquisition.

--de-identify

De-identify DICOM files, e-files and p-files prior to upload.

This flag removes the DICOM tags PatientID, PatientName, and PatientBirthDate.

--profile PROFILE

Use the de-identification profile to de-id more fields. See our article to learn more about creating this file.

--subject subject_label

Override value for the subject label

--session session_label

Override value for the session label