Centers the lab works with
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 and clusters the lab computes on, and how to obtain access.
Overview of CNT systems · Accessing Borel over SSH · Submitting jobs with SLURM · PMACS VPN
Imaging
Clinical imaging pulls, conversion of scans to NIfTI, and reconstruction of electrode positions. Scheduling and scanner-day work is in the CNT manual.
RADAR data pulls · DICOM to NIfTI · Electrode reconstruction · Grid labeling conventions
Electrophysiology
Intracranial EEG from export out of Natus through channel mapping, conversion and publication on ieeg.org, and its archiving.
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, and adding people to IRB studies. Consent, scheduling, reimbursement and testing are in the CNT manual.
Onboarding and offboarding · Adding personnel to an IRB study · Requesting a REDCap account · ieeg.org portal access
Procedures that are the CNT's alone, such as consenting, scanner-day and participant-facing coordinator work, live in the CNT procedures manual. Pages kept in both manuals say so at the top.
Lab Manual
An account of how the lab works, written for someone in their first week. It explains and points; the procedures themselves are in the six sections above.
- Start here
- What this lab is: mission, place within Penn, partner centers
- Roles in the lab: coordinators, research assistants, postdocs, students
- How data moves through the lab
- Regulatory and privacy essentials
- Glossary
By stage and by role
The procedures can also be read in the order data moves through the lab, or by the role that performs them.
- Map: a graph of the procedures by system, by stage, or by role
- Tags: every procedure listed under its stage and roles
- Roles: what each role is expected to know
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.