Pages by stage and role¶
Every procedure is tagged with its data-lifecycle stage (one of four) and the roles it serves. The lists below are generated from page front matter.
Clinical research coordinator / clinical RA¶
- 3T Consent Script
- 3T Research Scans: Scheduling & Billing
- 7T Badge Access & MRI Safety Training
- 7T Consent Script
- 7T Research Scans: Logistics & Safety
- Adding CAMRIS Users
- Adding Personnel to an IRB Study
- Adding Staff to the Penn+Box CNT Administration Folder
- Adding Users to the ieeg.org Portal
- Adding a Non-Penn / New Hire to a Study
- All Consent Forms (Box links)
- Archive: 7T Scans
- Archive: fMRI/3T Scans
- Archive: sEEG Implants
- Bedside Testing: Gold Audio Task
- CNT Data & Computing Orientation
- CRC Access Checklist (systems, badges, trainings)
- Citrix Remote Desktop Access
- Clipping Gold Audio Task Files in Natus
- Closing an IRB Study
- Consent Note Templates
- Consent Signing Checklist
- Contacting & Scheduling Patients
- Control Scan Neuroradiologist Check
- Creating a Greenphire Account
- Creating a New Study
- Email Template: Scheduling a Research 3T with Radiology
- Exporting EEG from Natus via VNC (Pioneer)
- Exporting Files from Natus
- Flywheel → cnt-fs (3T)
- Giving a User Study Access
- Greenphire ClinCard: Overview
- How the e-Consent Form Works
- Implant Coordinator Email & EMU Testing Slots
- Important Contacts & Emergency Numbers
- Increasing a Study Budget
- Mapping the EMU Shared Drive
- Messaging in PennChart
- Neuropsych Battery: Materials
- Old → New REDCap Field Mapping
- Onboarding & Offboarding Checklist
- One HUP Pavilion Training
- Ordering Physical Cards
- Path BioResource Manager Access
- Pedro → cnt-fs (7T)
- PennChart Research Billing Review
- PennChart Training
- PennKey & REDCap Access for External Guests
- Postop Neuropsych Testing: Overview
- REDCap Documentation at the Scanner
- REDCap Tips
- RPPR Demographic Tables
- RPPR: Dates, Targets & Milestones
- Reimbursing a Participant
- Remote Access to the Hayden Hall UPHS Computer
- Remote e-Consent Procedure
- Requesting Shared Drive Access (Penn Medicine ticket)
- Requesting a REDCap Account
- Running the 7T
- Running the Test
- Running the fMRI
- Scan Scheduling Trackers (sEEG, 3T/fMRI, 7T)
- Scoring
- Seizure Terminology Reference
- Sending the Signed ICF & Attestation
- Surgical Outcomes REDCap Project
- Testing Battery
- Triggering REDCap Scale Invites
- UPHS F5 VPN Access
- Updating CAMRIS User Access
- Uploading MRI CDs to cnt-fs
- Visit Checklist: 3T Study
- Visit Checklist: 7T Study
- e-Regulatory Binder & eDoA (Audit Prep)
- eDOA REDCap Entry
Data Analytics¶
- AWS @ Penn: Getting Started
- Accessing Borel over SSH
- BSC Cluster
- CNT Computing Schematic
- EMU Interictal Scalp EEG Pipeline
- EMU Interictal Scalp EEG Pipeline (duplicate — merge)
- Git on the VDI & UPHS Computers
- Hayden Hall UPHS Computers
- Linux Command Shortcuts
- Mounting Leif over SMB
- Overview of CNT Systems
- PMACS LPC Welcome Email
- PMACS Overview
- PMACS VPN
- PennLINC BABS & ModelArray
- SEAS Servers: Borel, Leif, Pioneer
- SLURM on Finkel: Configuration & Limits
- Software Tools Index
- Submitting CETS & PMACS Helpdesk Tickets
- Submitting Jobs with SLURM
- VDI, cnt-fs and cnt1
- cntgpu1 GPU Queue
Data Collection¶
- 3T Consent Script
- 3T Research Scans: Scheduling & Billing
- 7T Consent Script
- 7T Research Scans: Logistics & Safety
- All Consent Forms (Box links)
- Archive: 7T Scans
- Archive: fMRI/3T Scans
- Archive: sEEG Implants
- Bedside Testing: Gold Audio Task
- Clipping Gold Audio Task Files in Natus
- Consent Note Templates
- Consent Signing Checklist
- Contacting & Scheduling Patients
- Control Scan Neuroradiologist Check
- Creating a Greenphire Account
- Creating a New Study
- Email Template: Scheduling a Research 3T with Radiology
- Exporting EEG from Natus via VNC (Pioneer)
- Exporting Files from Natus
- Flywheel → cnt-fs (3T)
- Giving a User Study Access
- Greenphire ClinCard: Overview
- How the e-Consent Form Works
- IC-CoDE Neuropsych (RADAR)
- Implant Coordinator Email & EMU Testing Slots
- Increasing a Study Budget
- Messaging in PennChart
- Neuropsych Battery: Materials
- Ordering Physical Cards
- Pedro → cnt-fs (7T)
- PennChart Research Billing Review
- Postop Neuropsych Testing: Overview
- RADAR Data Pulls
- RADAR Pull → REDCap Entry
- REDCap Documentation at the Scanner
- REDCap Tips
- Reimbursing a Participant
- Remote e-Consent Procedure
- Running the 7T
- Running the Test
- Running the fMRI
- Scan Scheduling Trackers (sEEG, 3T/fMRI, 7T)
- Scoring
- Sending the Signed ICF & Attestation
- Surgical Outcomes REDCap Project
- Testing Battery
- Triggering REDCap Scale Invites
- Uploading MRI CDs to cnt-fs
- Visit Checklist: 3T Study
- Visit Checklist: 7T Study
- natusdir & Data Collection Files
Data Governance¶
- 7T Badge Access & MRI Safety Training
- Adding CAMRIS Users
- Adding Personnel to an IRB Study
- Adding Staff to the Penn+Box CNT Administration Folder
- Adding Users to the ieeg.org Portal
- Adding a Non-Penn / New Hire to a Study
- Archiving EEG Data to Azure
- Archiving ieeg Files
- Azure Portal & Storage Tiers
- CNT Data & Computing Orientation
- CRC Access Checklist (systems, badges, trainings)
- Citrix Remote Desktop Access
- Closing an IRB Study
- Data Storage Locations
- De-Identifying EDF Headers
- De-Identifying EDFs
- De-identifying NIfTI Headers
- Deleting a Dataset from ieeg.org
- Important Contacts & Emergency Numbers
- Mapping the EMU Shared Drive
- Onboarding & Offboarding Checklist
- One HUP Pavilion Training
- Path BioResource Manager Access
- PennBox
- PennChart Training
- PennKey & REDCap Access for External Guests
- RPPR Demographic Tables
- RPPR: Dates, Targets & Milestones
- Re-uploading Archived Datasets
- Remote Access to the Hayden Hall UPHS Computer
- Requesting Shared Drive Access (Penn Medicine ticket)
- Requesting a REDCap Account
- UPHS F5 VPN Access
- Unarchiving an ieeg Dataset
- Updating CAMRIS User Access
- Where 3T and 7T Scans Are Stored
- cnt1 Scripts for Azure Archiving & Unarchiving
- e-Regulatory Binder & eDoA (Audit Prep)
- eDOA REDCap Entry
Data Standardization & Integration¶
- AWS Bucket Numbers (ieeg.org / PREVeNT)
- Adding an iEEG File to a Project
- Anonymize & Upload EDFs to ieeg.org
- Automated Channel Mapping
- Automated Channel Mappings for Natus EEG
- CHOP Stim Seizures EEG Processing
- Channel Mapping for EDFs (ieeg-dataset.ini)
- DICOM → NIfTI (non-BIDS)
- Electrode Reconstruction: Prep & Software
- Epilog ESI Protocol
- Final Step: Delete mef Folders
- GUI/Docker Reconstruction Workflow
- Grid Electrode Labeling Conventions
- MUSC Reconstruction
- Manual Channel Mapping (legacy)
- Mounting cnt-fs
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Moving Imaging Data Across CNT Servers
- Mxene EEG Processing & Upload
- Old → New REDCap Field Mapping
- Opening ITK-SNAP Files from PennBox
- Pennsieve Data Access Rules
- Pennsieve Downloader
- Processing for ieeg.org (natus2mef → validate → upload)
- Restarting ieeg.org
- Restarting the ieeg.org AWS Server
- Seizure Terminology Reference
- Setup for Processing
- Splitting Datasets
- The cnt-pipeline AWS Instance
- The config Folder
- The ieeg.properties File
- Transferring Files from Box to cnt-fs (rclone)
- Troubleshooting Processing Errors
- Uploading from cnt1 to Pennsieve
- Uploading to Pennsieve Locally
- sEEG Phase II Processing: Overview & Timeline
Data research coordinator / data RA¶
- AWS Bucket Numbers (ieeg.org / PREVeNT)
- Adding CAMRIS Users
- Adding Staff to the Penn+Box CNT Administration Folder
- Adding Users to the ieeg.org Portal
- Adding an iEEG File to a Project
- Anonymize & Upload EDFs to ieeg.org
- Archiving EEG Data to Azure
- Automated Channel Mapping
- Automated Channel Mappings for Natus EEG
- Azure Portal & Storage Tiers
- BSC Cluster
- CHOP Stim Seizures EEG Processing
- CNT Computing Schematic
- CNT Data & Computing Orientation
- CRC Access Checklist (systems, badges, trainings)
- Channel Mapping for EDFs (ieeg-dataset.ini)
- Citrix Remote Desktop Access
- Clipping Gold Audio Task Files in Natus
- DICOM → NIfTI (non-BIDS)
- Data Storage Locations
- De-Identifying EDF Headers
- De-Identifying EDFs
- De-identifying NIfTI Headers
- Deleting a Dataset from ieeg.org
- Electrode Reconstruction: Prep & Software
- Epilog ESI Protocol
- Exporting EEG from Natus via VNC (Pioneer)
- Exporting Files from Natus
- Final Step: Delete mef Folders
- Flywheel → cnt-fs (3T)
- GUI/Docker Reconstruction Workflow
- Git on the VDI & UPHS Computers
- Grid Electrode Labeling Conventions
- Hayden Hall UPHS Computers
- IC-CoDE Neuropsych (RADAR)
- Important Contacts & Emergency Numbers
- Linux Command Shortcuts
- MUSC Reconstruction
- Manual Channel Mapping (legacy)
- Mapping the EMU Shared Drive
- Messaging in PennChart
- Mounting cnt-fs
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Moving Imaging Data Across CNT Servers
- Mxene EEG Processing & Upload
- Old → New REDCap Field Mapping
- Onboarding & Offboarding Checklist
- One HUP Pavilion Training
- Opening ITK-SNAP Files from PennBox
- Overview of CNT Systems
- PMACS LPC Welcome Email
- PMACS Overview
- PMACS VPN
- Path BioResource Manager Access
- Pedro → cnt-fs (7T)
- PennBox
- PennChart Training
- PennKey & REDCap Access for External Guests
- PennLINC BABS & ModelArray
- Pennsieve Data Access Rules
- Pennsieve Downloader
- Processing for ieeg.org (natus2mef → validate → upload)
- RADAR Data Pulls
- RADAR Pull → REDCap Entry
- REDCap Tips
- Remote Access to the Hayden Hall UPHS Computer
- Requesting Shared Drive Access (Penn Medicine ticket)
- Requesting a REDCap Account
- Restarting ieeg.org
- Seizure Terminology Reference
- Setup for Processing
- Software Tools Index
- Splitting Datasets
- Submitting CETS & PMACS Helpdesk Tickets
- Surgical Outcomes REDCap Project
- The cnt-pipeline AWS Instance
- The config Folder
- The ieeg.properties File
- Transferring Files from Box to cnt-fs (rclone)
- Triggering REDCap Scale Invites
- Troubleshooting Processing Errors
- UPHS F5 VPN Access
- Updating CAMRIS User Access
- Uploading MRI CDs to cnt-fs
- Uploading from cnt1 to Pennsieve
- Uploading to Pennsieve Locally
- VDI, cnt-fs and cnt1
- Where 3T and 7T Scans Are Stored
- cnt1 Scripts for Azure Archiving & Unarchiving
- cntgpu1 GPU Queue
- natusdir & Data Collection Files
- sEEG Phase II Processing: Overview & Timeline
External collaborator¶
- AWS Bucket Numbers (ieeg.org / PREVeNT)
- Important Contacts & Emergency Numbers
- Pennsieve Data Access Rules
- Pennsieve Downloader
- Uploading from cnt1 to Pennsieve
- Uploading to Pennsieve Locally
PI / lab manager¶
- Adding CAMRIS Users
- Adding Personnel to an IRB Study
- Adding Staff to the Penn+Box CNT Administration Folder
- Adding Users to the ieeg.org Portal
- Adding a Non-Penn / New Hire to a Study
- CNT Data & Computing Orientation
- CRC Access Checklist (systems, badges, trainings)
- Citrix Remote Desktop Access
- Closing an IRB Study
- Creating a Greenphire Account
- Creating a New Study
- Data Storage Locations
- Giving a User Study Access
- Greenphire ClinCard: Overview
- Important Contacts & Emergency Numbers
- Increasing a Study Budget
- Mapping the EMU Shared Drive
- Onboarding & Offboarding Checklist
- One HUP Pavilion Training
- Ordering Physical Cards
- Path BioResource Manager Access
- PennBox
- PennChart Training
- PennKey & REDCap Access for External Guests
- Pennsieve Data Access Rules
- RPPR Demographic Tables
- RPPR: Dates, Targets & Milestones
- Reimbursing a Participant
- Remote Access to the Hayden Hall UPHS Computer
- Requesting Shared Drive Access (Penn Medicine ticket)
- Requesting a REDCap Account
- UPHS F5 VPN Access
- Updating CAMRIS User Access
- Where 3T and 7T Scans Are Stored
- e-Regulatory Binder & eDoA (Audit Prep)
- eDOA REDCap Entry
Pipeline & systems maintainer¶
- AWS @ Penn: Getting Started
- Accessing Borel over SSH
- Adding CAMRIS Users
- Adding Staff to the Penn+Box CNT Administration Folder
- Adding Users to the ieeg.org Portal
- Adding an iEEG File to a Project
- Anonymize & Upload EDFs to ieeg.org
- Archiving EEG Data to Azure
- Archiving ieeg Files
- Automated Channel Mapping
- Automated Channel Mappings for Natus EEG
- Azure Portal & Storage Tiers
- BSC Cluster
- CHOP Stim Seizures EEG Processing
- CNT Computing Schematic
- CRC Access Checklist (systems, badges, trainings)
- Channel Mapping for EDFs (ieeg-dataset.ini)
- Citrix Remote Desktop Access
- De-Identifying EDF Headers
- De-Identifying EDFs
- De-identifying NIfTI Headers
- Deleting a Dataset from ieeg.org
- EMU Interictal Scalp EEG Pipeline
- EMU Interictal Scalp EEG Pipeline (duplicate — merge)
- Epilog ESI Protocol
- Final Step: Delete mef Folders
- Hayden Hall UPHS Computers
- Important Contacts & Emergency Numbers
- Manual Channel Mapping (legacy)
- Mapping the EMU Shared Drive
- Mounting Leif over SMB
- Mounting cnt-fs
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Moving Imaging Data Across CNT Servers
- Mxene EEG Processing & Upload
- Onboarding & Offboarding Checklist
- Overview of CNT Systems
- PMACS LPC Welcome Email
- PMACS Overview
- PMACS VPN
- Path BioResource Manager Access
- PennKey & REDCap Access for External Guests
- Processing for ieeg.org (natus2mef → validate → upload)
- Re-uploading Archived Datasets
- Remote Access to the Hayden Hall UPHS Computer
- Requesting Shared Drive Access (Penn Medicine ticket)
- Requesting a REDCap Account
- Restarting ieeg.org
- Restarting the ieeg.org AWS Server
- SEAS Servers: Borel, Leif, Pioneer
- SLURM on Finkel: Configuration & Limits
- Setup for Processing
- Splitting Datasets
- Submitting CETS & PMACS Helpdesk Tickets
- Submitting Jobs with SLURM
- The cnt-pipeline AWS Instance
- The config Folder
- The ieeg.properties File
- Transferring Files from Box to cnt-fs (rclone)
- Troubleshooting Processing Errors
- UPHS F5 VPN Access
- Unarchiving an ieeg Dataset
- Updating CAMRIS User Access
- VDI, cnt-fs and cnt1
- cnt1 Scripts for Azure Archiving & Unarchiving
- cntgpu1 GPU Queue
- natusdir & Data Collection Files
- sEEG Phase II Processing: Overview & Timeline
Trainee / analyst (postdoc, PhD, master's, undergraduate)¶
- AWS Bucket Numbers (ieeg.org / PREVeNT)
- Accessing Borel over SSH
- Adding CAMRIS Users
- Adding Staff to the Penn+Box CNT Administration Folder
- Adding Users to the ieeg.org Portal
- BSC Cluster
- CNT Computing Schematic
- CRC Access Checklist (systems, badges, trainings)
- Citrix Remote Desktop Access
- DICOM → NIfTI (non-BIDS)
- Data Storage Locations
- EMU Interictal Scalp EEG Pipeline
- EMU Interictal Scalp EEG Pipeline (duplicate — merge)
- Electrode Reconstruction: Prep & Software
- GUI/Docker Reconstruction Workflow
- Git on the VDI & UPHS Computers
- Grid Electrode Labeling Conventions
- Hayden Hall UPHS Computers
- Important Contacts & Emergency Numbers
- Linux Command Shortcuts
- MUSC Reconstruction
- Mapping the EMU Shared Drive
- Mounting Leif over SMB
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Moving Imaging Data Across CNT Servers
- Onboarding & Offboarding Checklist
- Opening ITK-SNAP Files from PennBox
- Overview of CNT Systems
- PMACS LPC Welcome Email
- PMACS Overview
- PMACS VPN
- Path BioResource Manager Access
- PennBox
- PennKey & REDCap Access for External Guests
- PennLINC BABS & ModelArray
- Pennsieve Downloader
- Remote Access to the Hayden Hall UPHS Computer
- Requesting Shared Drive Access (Penn Medicine ticket)
- Requesting a REDCap Account
- SEAS Servers: Borel, Leif, Pioneer
- SLURM on Finkel: Configuration & Limits
- Software Tools Index
- Submitting CETS & PMACS Helpdesk Tickets
- Submitting Jobs with SLURM
- Transferring Files from Box to cnt-fs (rclone)
- UPHS F5 VPN Access
- Updating CAMRIS User Access
- Uploading from cnt1 to Pennsieve
- Uploading to Pennsieve Locally
- VDI, cnt-fs and cnt1
- Where 3T and 7T Scans Are Stored
- cntgpu1 GPU Queue