Overview

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:

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.