Below are additional examples of templates. Use these as a starting point for your own ingest template.
Uploading JPG files
The template is a good option if you want to upload non-DICOM data to Flywheel. Note that the packfile_type can be any filetype
template: - pattern: "{subject}" - pattern: "{session}" - pattern: ".*" - pattern: "{acquisition}" packfile_type: jpg
The template below pulls out the subject and session labels from the first folder name, skips a level, uses the 3rd folder name as the acquisition label, and then uses the dicom scan to validate DICOM files before upload:
template: - pattern: "wimrpetct{subject}_{session}" - pattern: ".*" - pattern: "{acquisition}" scan: name: dicom
The example below uses folder names to set 2 different custom metadata fields.
- pattern: "{session.info.dataset}" - pattern: "XR_{acquisition}" - pattern: "patient{subject}" - pattern: "study{session}_{acquisition.info.outcome}"
The custom metadata fields are called dataset , which is stored in the session, and the other is called outcome, which is stored on the acquisition.
The template below uses the filename from the imaging data to label the acquisitions in Flywheel.
--- - pattern: "{subject}" - pattern: "{session}" scan: name: filename pattern: "^(?:[^_]*_){3}(?P<acquisition>[^.]*)"
Original Filename |
Flywheel Acquisition label |
20210214_164316_SubjectName_AcqParameter1_AcqParameter2_AcqParameter3.mhd |
AcqParameter1_AcqParameter2_AcqParameter3 |
Regex can quickly become complicated. You can test out your filename and regex using an online tool such as regex101.
Click Next to de-identify your dataset with a custom de-id profile.