Data
Where the lab's data is kept and how it is laid out, moved between servers, archived to Azure, shared through Pennsieve and ieeg.org, and de-identified.
Data storage locations · Moving data across servers · De-identifying EDFs · Uploading to Pennsieve
Compute
The servers, clusters and cloud accounts the lab computes on, the software installed on them, and how to obtain access.
Overview of CNT systems · Accessing Borel over SSH · Submitting jobs with SLURM · PMACS VPN
Imaging
MRI and CT, from scheduling a scan through the scanner session, transfer of the images, conversion to NIfTI and reconstruction of electrode positions.
Visit checklist for a 3T study · Running the 7T · Flywheel to cnt-fs · Electrode reconstruction
Electrophysiology
Scalp and intracranial EEG, from acquisition in the epilepsy monitoring unit through export from Natus, channel mapping and publication on ieeg.org.
Exporting files from Natus · Automated channel mapping · Processing for ieeg.org · Phase II timeline
REDCap & Clinical Metadata
The REDCap projects that hold clinical variables, the conventions for entering data in them, and the pulls from the electronic health record that feed them.
Surgical Outcomes project · REDCap tips · RADAR pull to REDCap · Seizure terminology
Operations
Accounts and access, onboarding and offboarding, IRB submissions, consent, scheduling, participant reimbursement, neuropsychological testing and contacts.
Access checklist · Onboarding and offboarding · Adding personnel to an IRB study · Consent signing checklist
Reading by role
Every procedure is tagged with the roles that perform it. Clinical research coordinators begin with Operations and Imaging; data staff with Data, Compute and Electrophysiology.
Contributing
To correct a page, use the edit button at the top of it, or edit the Markdown in Obsidian and commit. See how contributing works, the style guide and the SOP template. Pages flagged by the October 2026 audit carry a banner; the full list is in AUDIT.md in the repository.