-h

Show this help message and exit

--config-file CONFIG_FILE

Specify configuration options via config file

--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

--jobs JOBS

The number of concurrent jobs to run (e.g. compression jobs)

--concurrent-uploads CONCURRENT_UPLOADS

The maximum number of concurrent uploads

--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

--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 dicoms 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.

--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 your custom de-id profile.

 See our article to learn more about creating this profile.

--group <id>

Configure group id

--project <label>

Configure project label

--dicom name

The name of dicom subfolders to be zipped prior to upload.

--pack-acquisitions type

Acquisition folders only contain acquisitions of the designated type and are zipped prior to upload.

--repack

Validate, de-identify, and zip files.

--no-subjects

Import data without subjects

--no-sessions

import data without sessions

--set-var key=value -s key=value

Manually set the variable.

For example, to set the acquisition label: --set-var acquisition.label=Scan