Step 3: Include/exclude settings

#####
# Template Settings
#####

template:
  - pattern: "{subject}"
  - pattern: "{session}"
  - pattern: "{acquisition}"
    name:
      scan: dicom

####
# De-identification settings
####
name: Profile1
dicom:

  # Date-increment controls how many days to offset each date field
  # where the increment-date (shown below) is configured.
  #Positive values will result in later dates, negative
  # values will result in earlier dates.

  date-increment: -17

  # patient-age-from-birthdate sets the DICOM header as a 3-digit value with a suffix
  # be 091D, and that same age in months would be 003M. By default, if
  # the age fits in days, then days will be used,
  # otherwise if it fits in months, then months
  # will be used, otherwise years will be used

  patient-age-from-birthdate: true
  
  # all data elements not defined in fields section of the profile will be removed. 
  # If any field references a nested element in a sequence the whole sequence element 
  # will be kept.
  
  remove-undefined: true

  # Set patient age units as Years. Other options include months (M) and days (D)

  patient-age-units: Y

  # The following are field transformations.
  # Remove, replace-with, increment-date, hash, and hashuid can be used with any DICOM
  # field. Replace name with the DICOM field "keyword" by the DICOM standard
  fields:

    # Use remove Remove a dicom field Removes the field from the DICOM entirely.
    # If removal is not supported then this field will be blank.
    # This example removes PatientID.

    - name: PatientID
      replace-with: REDACTED

    # Replace a dicom field with the value provided.
    # This example replaces “StationName” with "XXXX" in Flywheel

    - name: StationName
      replace-with: XXXX

    # Offsets the date by the number of days defined in
    # the date-increment setting above, preserving the time
    # and timezone. In this example, StudyDate appears as 17 days earlier

    - name: StudyDate
      increment-date: true

    # You can refer to fields by their DICOM tag or keyword
    # Applies one-way hash to a unique string

    - name: (0008,0050)
      hash: true

     # Replaces a UID field with a hashed version of that
     # field. The first four nodes (prefix) and last node
     # (suffix) will be preserved, with the middle being
     # replaced by the hashed value

    - name: ConcatenationUID
      hashuid: true
    
    # The fields below are listed so that they are not removed as part of the 
    # remove-undefined setting above. 
    - name: SeriesInstanceUID
    - name: Modality
    - name: SeriesNumber
    - name: ScheduledProcedureStepID
    - name: RequestedProcedureID
    - name: StudyTime
    - name: StudyID
    - name: SeriesNumber
    - name: PatientID
    - name: StudyInstanceUID
    - name: ProtocolName
    - name: AcquisitionDate
      increment-date: true
    - name: AcquisitionDateTime
    - name: AcquisitionTime
    - name: SeriesDate
      increment-date: true
    - name: SeriesTime

####
# Include/Exclude Settings 
####

# Flywheel uploads only the new data and does not upload duplicates. 
# all duplicates are noted in the ingest audit log attached to the project

detect-duplicates: true

# Use regex to indicate file types to exclude from upload

exclude:  
  - "*.txt"
  - "*.xml"

# Use regex to indicate directories to include in upload
include-dirs:  
  - "*-DCM"

Click Next to learn how to run the ingest template command and upload your data.