If your directories are a mix of file formats and do not follow a standard structure, you can use the template import
to set rules for how to import data. See our directions for how to use the template import.
fw import template [Optional arguments] [template] [folder]
Required arguments reference
Required arguments |
Description |
---|---|
template |
The location of the YAML template or template string. |
folder |
The path to the folder to import |
Optional arguments reference
Optional Arguments |
Description |
---|---|
-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 |
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. 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). |
--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. If your DICOM files are compressed in to a zipped file, you should also use with --repack flag to de-identify the files. This flag removes the DICOM tags PatientID, PatientName, and PatientBirthDate. |
--profile PROFILE |
Use your custom de-id 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 |
Unzips archived DICOM files to validate and then repackages the DICOM files as zipped files to upload. |
--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 |