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CNT Procedures Manual

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CNT Procedures Manual

penn-cnt/cnt-procedures

Home
Data
Data
- Storage Locations
  Storage Locations
- Moving Data
  Moving Data
- Archiving (Azure)
  Archiving (Azure)
- Sharing (Pennsieve & ieeg.org)
  Sharing (Pennsieve & ieeg.org)
- De-identification
  De-identification
Compute
Compute
- Overview
  Overview
- SEAS (CETS) Servers
  SEAS (CETS) Servers
- PMACS (PSOM) Systems
  PMACS (PSOM) Systems
- Cloud (AWS)
  Cloud (AWS)
  - AWS @ Penn: Getting Started
  - Restarting the ieeg.org AWS Server
- Software & Tools
  Software & Tools
- Support & Tickets
  Support & Tickets
  - Submitting CETS & PMACS Helpdesk Tickets
Imaging
Imaging
- Scheduling & Visits
  Scheduling & Visits
- At the Scanner
  At the Scanner
- Post-scan Transfer
  Post-scan Transfer
- Formatting
  Formatting
  - DICOM → NIfTI (non-BIDS)
- Electrode Reconstruction
  Electrode Reconstruction
- Clinical Imaging Pulls (RADAR)
  Clinical Imaging Pulls (RADAR)
  - RADAR Data Pulls
Electrophysiology
Electrophysiology
- Overview & Setup
  Overview & Setup
- EMU Acquisition
  EMU Acquisition
  - Implant Coordinator Email & EMU Testing Slots
  - Bedside Testing: Gold Audio Task
- Exporting from Natus
  Exporting from Natus
- Channel Mapping
  Channel Mapping
- Processing & Upload to ieeg.org
  Processing & Upload to ieeg.org
- Archiving on ieeg.org
  Archiving on ieeg.org
- Scalp EEG
  Scalp EEG
  - EMU Interictal Scalp EEG Pipeline
  - EMU Interictal Scalp EEG Pipeline (duplicate — merge)
- Special Protocols
  Special Protocols
REDCap & Clinical Metadata
REDCap & Clinical Metadata
- Projects & Data Entry
  Projects & Data Entry
- Clinical Data Pulls (EHR → REDCap)
  Clinical Data Pulls (EHR → REDCap)
  - RADAR Pull → REDCap Entry
  - IC-CoDE Neuropsych (RADAR)
Operations
Operations
- Access & Accounts
  Access & Accounts
- Onboarding & Offboarding
  Onboarding & Offboarding
- Regulatory, IRB & Reporting
  Regulatory, IRB & Reporting
- Consenting
  Consenting
- Scheduling Trackers
  Scheduling Trackers
- Participant Reimbursement (Greenphire)
  Participant Reimbursement (Greenphire)
- Postop Neuropsych Testing
  Postop Neuropsych Testing
- Contacts
  Contacts
  - Important Contacts & Emergency Numbers
Map
Tags
About this wiki
About this wiki

Software & Tools¶

Git, Linux, analysis toolkits and the tools index.

Git on the VDI & UPHS Computers
Linux Command Shortcuts
PennLINC BABS & ModelArray
Software Tools Index

October 5, 2026

Restarting the ieeg.org AWS Server

Git on the VDI & UPHS Computers

Center for Neuroengineering & Therapeutics · internal use