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¶
- Adding Personnel to an IRB Study
- Adding Users to the ieeg.org Portal
- Adding a Non-Penn / New Hire to a Study
- Exporting Files from Natus
- Onboarding & Offboarding Checklist
- PennKey & REDCap Access for External Guests
- REDCap Tips
- Requesting a REDCap Account
- Seizure Terminology Reference
- Surgical Outcomes REDCap Project
Data Analytics¶
- Accessing Borel over SSH
- BSC Cluster
- Mounting Leif over SMB
- Overview of CNT Systems
- PMACS VPN
- SEAS Servers: Borel, Leif, Pioneer
- SLURM on Finkel: Configuration & Limits
- Submitting CETS & PMACS Helpdesk Tickets
- Submitting Jobs with SLURM
Data Collection¶
- Exporting Files from Natus
- RADAR Data Pulls
- RADAR Pull → REDCap Entry
- REDCap Tips
- Surgical Outcomes REDCap Project
- natusdir & Data Collection Files
Data Governance¶
- Adding Personnel to an IRB Study
- Adding Users to the ieeg.org Portal
- Adding a Non-Penn / New Hire to a Study
- Archiving EEG Data to Azure
- Archiving ieeg Files
- Data Storage Locations
- De-Identifying EDF Headers
- De-Identifying EDFs
- De-identifying NIfTI Headers
- Deleting a Dataset from ieeg.org
- Onboarding & Offboarding Checklist
- PennKey & REDCap Access for External Guests
- Re-uploading Archived Datasets
- Requesting a REDCap Account
- Unarchiving an ieeg Dataset
- cnt1 Scripts for Azure Archiving & Unarchiving
Data Standardization & Integration¶
- Adding an iEEG File to a Project
- Anonymize & Upload EDFs to ieeg.org
- Automated Channel Mapping
- Channel Mapping for EDFs (ieeg-dataset.ini)
- DICOM → NIfTI (non-BIDS)
- Electrode Reconstruction: Prep & Software
- Final Step: Delete mef Folders
- GUI/Docker Reconstruction Workflow
- Grid Electrode Labeling Conventions
- MUSC Reconstruction
- Mounting cnt-fs
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Pennsieve Data Access Rules
- Pennsieve Downloader
- Processing for ieeg.org (natus2mef → validate → upload)
- Seizure Terminology Reference
- Setup for Processing
- Splitting Datasets
- 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¶
- 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
- BSC Cluster
- Channel Mapping for EDFs (ieeg-dataset.ini)
- 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
- Exporting Files from Natus
- Final Step: Delete mef Folders
- GUI/Docker Reconstruction Workflow
- Grid Electrode Labeling Conventions
- MUSC Reconstruction
- Mounting cnt-fs
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Onboarding & Offboarding Checklist
- Overview of CNT Systems
- PMACS VPN
- PennKey & REDCap Access for External Guests
- Pennsieve Data Access Rules
- Pennsieve Downloader
- Processing for ieeg.org (natus2mef → validate → upload)
- RADAR Data Pulls
- RADAR Pull → REDCap Entry
- REDCap Tips
- Requesting a REDCap Account
- Seizure Terminology Reference
- Setup for Processing
- Splitting Datasets
- Submitting CETS & PMACS Helpdesk Tickets
- Surgical Outcomes REDCap Project
- 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
- cnt1 Scripts for Azure Archiving & Unarchiving
- natusdir & Data Collection Files
- sEEG Phase II Processing: Overview & Timeline
External collaborator¶
- Pennsieve Data Access Rules
- Pennsieve Downloader
- Uploading from cnt1 to Pennsieve
- Uploading to Pennsieve Locally
PI / lab manager¶
- Adding Personnel to an IRB Study
- Adding Users to the ieeg.org Portal
- Adding a Non-Penn / New Hire to a Study
- Data Storage Locations
- Onboarding & Offboarding Checklist
- PennKey & REDCap Access for External Guests
- Pennsieve Data Access Rules
- Requesting a REDCap Account
Pipeline & systems maintainer¶
- Accessing Borel over SSH
- 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
- BSC Cluster
- Channel Mapping for EDFs (ieeg-dataset.ini)
- De-Identifying EDF Headers
- De-Identifying EDFs
- De-identifying NIfTI Headers
- Deleting a Dataset from ieeg.org
- Final Step: Delete mef Folders
- Mounting Leif over SMB
- Mounting cnt-fs
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Onboarding & Offboarding Checklist
- Overview of CNT Systems
- PMACS VPN
- PennKey & REDCap Access for External Guests
- Processing for ieeg.org (natus2mef → validate → upload)
- Re-uploading Archived Datasets
- Requesting a REDCap Account
- 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 config Folder
- The ieeg.properties File
- Transferring Files from Box to cnt-fs (rclone)
- Troubleshooting Processing Errors
- Unarchiving an ieeg Dataset
- cnt1 Scripts for Azure Archiving & Unarchiving
- natusdir & Data Collection Files
- sEEG Phase II Processing: Overview & Timeline
Trainee / analyst (postdoc, PhD, master's, undergraduate)¶
- Accessing Borel over SSH
- Adding Users to the ieeg.org Portal
- BSC Cluster
- DICOM → NIfTI (non-BIDS)
- Data Storage Locations
- Electrode Reconstruction: Prep & Software
- GUI/Docker Reconstruction Workflow
- Grid Electrode Labeling Conventions
- MUSC Reconstruction
- Mounting Leif over SMB
- Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
- Onboarding & Offboarding Checklist
- Overview of CNT Systems
- PMACS VPN
- PennKey & REDCap Access for External Guests
- Pennsieve Downloader
- Requesting a REDCap Account
- SEAS Servers: Borel, Leif, Pioneer
- SLURM on Finkel: Configuration & Limits
- Submitting CETS & PMACS Helpdesk Tickets
- Submitting Jobs with SLURM
- Transferring Files from Box to cnt-fs (rclone)
- Uploading from cnt1 to Pennsieve
- Uploading to Pennsieve Locally