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Lab Manual
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NeuroBridge Lab Wiki
penn-neurobridge/neurobridge-wiki
Home
Lab Manual
Lab Manual
0. Start here
1. What this lab is
2. Roles in the lab
3. Getting set up: accounts and access
4. How data moves through the lab
5. Sites, centers and collaborators
6. Regulatory and privacy essentials
7. Rhythm, communication and writing SOPs
8. Glossary
9. Leaving the lab
Centers
Centers
Center for Neuroengineering & Therapeutics
Institute for Biomedical Informatics
Center for Clinical Epidemiology and Biostatistics
Penn Stroke Center and LCNS
Center for Brain Injury and Repair
CHOP Informatics
Data
Data
Storage Locations
Storage Locations
Data Storage Locations
Moving Data
Moving Data
Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
Transferring Files from Box to cnt-fs (rclone)
Archiving (Azure)
Archiving (Azure)
Archiving EEG Data to Azure
cnt1 Scripts for Azure Archiving & Unarchiving
Sharing (Pennsieve & ieeg.org)
Sharing (Pennsieve & ieeg.org)
Pennsieve Data Access Rules
Uploading to Pennsieve Locally
Uploading from cnt1 to Pennsieve
Pennsieve Downloader
De-identification
De-identification
De-Identifying EDFs
De-Identifying EDF Headers
De-identifying NIfTI Headers
Compute
Compute
Overview
Overview
Overview of CNT Systems
SEAS (CETS) Servers
SEAS (CETS) Servers
SEAS Servers: Borel, Leif, Pioneer
Accessing Borel over SSH
Mounting Leif over SMB
Submitting Jobs with SLURM
SLURM on Finkel: Configuration & Limits
PMACS (PSOM) Systems
PMACS (PSOM) Systems
BSC Cluster
PMACS VPN
Support & Tickets
Support & Tickets
Submitting CETS & PMACS Helpdesk Tickets
Imaging
Imaging
Formatting
Formatting
DICOM → NIfTI (non-BIDS)
Electrode Reconstruction
Electrode Reconstruction
Electrode Reconstruction: Prep & Software
GUI/Docker Reconstruction Workflow
MUSC Reconstruction
Grid Electrode Labeling Conventions
Clinical Imaging Pulls (RADAR)
Clinical Imaging Pulls (RADAR)
RADAR Data Pulls
Electrophysiology
Electrophysiology
Overview & Setup
Overview & Setup
sEEG Phase II Processing: Overview & Timeline
Setup for Processing
Mounting cnt-fs
natusdir & Data Collection Files
The config Folder
The ieeg.properties File
Exporting from Natus
Exporting from Natus
Exporting Files from Natus
Channel Mapping
Channel Mapping
Automated Channel Mapping
Channel Mapping for EDFs (ieeg-dataset.ini)
Processing & Upload to ieeg.org
Processing & Upload to ieeg.org
Processing for ieeg.org (natus2mef → validate → upload)
Troubleshooting Processing Errors
Anonymize & Upload EDFs to ieeg.org
Adding an iEEG File to a Project
Splitting Datasets
Final Step: Delete mef Folders
Deleting a Dataset from ieeg.org
Archiving on ieeg.org
Archiving on ieeg.org
Archiving ieeg Files
Unarchiving an ieeg Dataset
Re-uploading Archived Datasets
REDCap & Clinical Metadata
REDCap & Clinical Metadata
Projects & Data Entry
Projects & Data Entry
Surgical Outcomes REDCap Project
Seizure Terminology Reference
REDCap Tips
Clinical Data Pulls (EHR → REDCap)
Clinical Data Pulls (EHR → REDCap)
RADAR Pull → REDCap Entry
Operations
Operations
Access & Accounts
Access & Accounts
PennKey & REDCap Access for External Guests
Requesting a REDCap Account
Adding Users to the ieeg.org Portal
Onboarding & Offboarding
Onboarding & Offboarding
Onboarding & Offboarding Checklist
Regulatory, IRB & Reporting
Regulatory, IRB & Reporting
Adding Personnel to an IRB Study
Adding a Non-Penn / New Hire to a Study
Map
Tags
About this wiki
About this wiki
Contributing
Style guide
SOP template
Roles
Formatting
¶
DICOM to NIfTI conversion outside BIDS.
DICOM → NIfTI (non-BIDS)
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