CLI reference guide: import bruker

folder

The location of the parent folder containing the data you want to import

group_id

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

project_label

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

-h

Show this help message and exit

--config-file CONFIG_FILE

Specify configuration options via config file. Learn more about 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

Turns off 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.

--exclude EXCLUDE

Enter specific filenames or use wildcard matches (?,*) to exclude patterns of filenames.

--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

Path to a private dicom file. Learn more about how to create this file to de-identify your data.

--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.

--folder-template FOLDER TEMPLATE

Optional folder template