The config file is used with the ingest template
command to upload data. This upload method allows you to leverage the existing folder structure in your local server to map your dataset to a Flywheel project. The alternative is to use an upload method that organizes files based on the file's metadata (such as with the ingest dicom
command.)
This article explains how to create a config file to use with the ingest template
command so you can:
Organize and label your folders and files to map to a Flywheel project
Include/exclude files and folders for upload
De-identify your data if necessary using a de-id profile
Below is an example of the ingest template command and a config file. This guide will cover each section of the config in more detail.
fw ingest template -C MyConfig.yaml /path/to/data --group [group.id] --project [project label]
##### # Template and Group/Project Settings ##### template: - pattern: "{project}" - pattern: "{subject}" - pattern: "{session}" - pattern: "{acquisition}" scan: dicom ##### # Includes/excludes directories or file types ##### # Patterns of directories to include include-dirs: - "*-DCM" # Patterns of filenames to exclude exclude: - "*.txt" - "*.xml" ##### # De-identification Settings ##### deid-profile: custom deid-profiles: - name: custom dicom: # What date offset to use, in number of days date-increment: -17 # Remove all private tags remove-private-tags: true # Set patient age from date of birth patient-age-from-birthdate: true # Set patient age units as Years patient-age-units: Y fields: # Remove a dicom field (e.g.remove PatientID) - name: PatientID remove: true # Increment a date field by -17 days - name: StudyDate increment-date: true # One-Way hash a dicom field to a unique string - name: AccessionNumber hash: true
Click Next to start creating a template section for the config file.