CLI Reference Guide: Import Par/Rec Files
Introduction
If you have folders that include PAR/REC files, you can use the corresponding import option. The import parrec command can be used on directories that include other file types. The Flywheel CLI searches for the .par and .rec file extensions and imports just those files.
Usage
fw import parrec [optional arguments] folder group_id project_label
Tip
By default, Flywheel uses Examination name for the subject label. If you want to use a different subject label within Flywheel, use the --subject flag.
Instruction Steps
Required Arguments
| Required arguments | Description |
|---|---|
| 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 project label or enter a new project label to create the project when you import data. |
Optional Arguments
| Optional Arguments | Description |
|---|---|
| -h | Show this help message and exit |
| --config-file CONFIG_FILE | Uses the config file to set the flags for the command. Learn more about how to create and use the config file to set optional flags for commands. |
| --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 | 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 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. |
| --subject SUBJECT_LABEL | Override value for the subject label |
| --session SESSION_LABEL | Override value for the session label |