Example Processing Procedures

This chapter details common processing procedures that utilize the tools described within the manaual. A sample project has an IRB protocol number of 2022.001. Since a period (‘.’) is an illegal character for the <project_identifier>, we will specify 2022-001 as the <project_identifier> for the examples provided herein. You should work with Dr. Sherwood to determine your project identifier.

Project Startup

Modify credentials JSON control file

Edit the credentials.json file located at /resshare/general_processing_code

1. Add 2022-001 to the “projects” key

2. Create a new key titled 2022-001

3. Add the elements from Dictionary keys for the <project_identifier> elements to the 2022-001 dictionary

Create MySQL tables

Create the Project’s MySQL tables

$ connect_create_project_db.py -p 2022-001

Create a scan ID JSON control file

Create the Project’s scan ID JSON file in the Project’s code directory

Note

You may want to first collect a set of Pilot mri data and transmit to the CoNNECT NPC via PACS after you have completed the previous steps, then evaluate the JSON sidecar files in the sourcedata directory after DICOM conversion to select unique key/value pairs for each NIfTI image. This DICOM-to-NIfTI conversion should be completed automatically upon data transfer as part of the pacs-grabber service; however, creation of the BIDS-formatted rawdata will fail as this requires the Project’s scan ID JSON file.