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CNT Procedures Manual
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CNT Procedures Manual
penn-cnt/cnt-procedures
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Data
Data
Storage Locations
Storage Locations
Data Storage Locations
Where 3T and 7T Scans Are Stored
PennBox
Moving Data
Moving Data
Moving Data Across cnt-fs, cnt1, BSC, Borel & Leif
Moving Imaging Data Across CNT Servers
Transferring Files from Box to cnt-fs (rclone)
Archiving (Azure)
Archiving (Azure)
Archiving EEG Data to Azure
cnt1 Scripts for Azure Archiving & Unarchiving
Azure Portal & Storage Tiers
Sharing (Pennsieve & ieeg.org)
Sharing (Pennsieve & ieeg.org)
Pennsieve Data Access Rules
Uploading to Pennsieve Locally
Uploading from cnt1 to Pennsieve
Pennsieve Downloader
AWS Bucket Numbers (ieeg.org / PREVeNT)
De-identification
De-identification
De-Identifying EDFs
De-Identifying EDF Headers
De-identifying NIfTI Headers
Compute
Compute
Overview
Overview
Overview of CNT Systems
CNT Computing Schematic
VDI, cnt-fs and cnt1
Hayden Hall UPHS Computers
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
PMACS Overview
PMACS LPC Welcome Email
BSC Cluster
cntgpu1 GPU Queue
PMACS VPN
Cloud (AWS)
Cloud (AWS)
AWS @ Penn: Getting Started
Restarting the ieeg.org AWS Server
Software & Tools
Software & Tools
Git on the VDI & UPHS Computers
Linux Command Shortcuts
PennLINC BABS & ModelArray
Software Tools Index
Support & Tickets
Support & Tickets
Submitting CETS & PMACS Helpdesk Tickets
Imaging
Imaging
Scheduling & Visits
Scheduling & Visits
Visit Checklist: 3T Study
Visit Checklist: 7T Study
Email Template: Scheduling a Research 3T with Radiology
3T Research Scans: Scheduling & Billing
7T Research Scans: Logistics & Safety
At the Scanner
At the Scanner
Running the 7T
7T Badge Access & MRI Safety Training
Running the fMRI
REDCap Documentation at the Scanner
PennChart Research Billing Review
Control Scan Neuroradiologist Check
Post-scan Transfer
Post-scan Transfer
Flywheel → cnt-fs (3T)
Pedro → cnt-fs (7T)
Uploading MRI CDs to cnt-fs
Formatting
Formatting
DICOM → NIfTI (non-BIDS)
Electrode Reconstruction
Electrode Reconstruction
Electrode Reconstruction: Prep & Software
GUI/Docker Reconstruction Workflow
MUSC Reconstruction
Opening ITK-SNAP Files from PennBox
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
EMU Acquisition
EMU Acquisition
Implant Coordinator Email & EMU Testing Slots
Bedside Testing: Gold Audio Task
Exporting from Natus
Exporting from Natus
Exporting Files from Natus
Exporting EEG from Natus via VNC (Pioneer)
Clipping Gold Audio Task Files in Natus
Channel Mapping
Channel Mapping
Automated Channel Mapping
Automated Channel Mappings for Natus EEG
Manual Channel Mapping (legacy)
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
The cnt-pipeline AWS Instance
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
Restarting ieeg.org
Archiving on ieeg.org
Archiving on ieeg.org
Archiving ieeg Files
Unarchiving an ieeg Dataset
Re-uploading Archived Datasets
Scalp EEG
Scalp EEG
EMU Interictal Scalp EEG Pipeline
EMU Interictal Scalp EEG Pipeline (duplicate — merge)
Special Protocols
Special Protocols
Mxene EEG Processing & Upload
CHOP Stim Seizures EEG Processing
Epilog ESI Protocol
REDCap & Clinical Metadata
REDCap & Clinical Metadata
Projects & Data Entry
Projects & Data Entry
Surgical Outcomes REDCap Project
Messaging in PennChart
Seizure Terminology Reference
Triggering REDCap Scale Invites
Old → New REDCap Field Mapping
REDCap Tips
Clinical Data Pulls (EHR → REDCap)
Clinical Data Pulls (EHR → REDCap)
RADAR Pull → REDCap Entry
IC-CoDE Neuropsych (RADAR)
Operations
Operations
Access & Accounts
Access & Accounts
CRC Access Checklist (systems, badges, trainings)
UPHS F5 VPN Access
Citrix Remote Desktop Access
Remote Access to the Hayden Hall UPHS Computer
Requesting Shared Drive Access (Penn Medicine ticket)
Mapping the EMU Shared Drive
PennKey & REDCap Access for External Guests
Requesting a REDCap Account
Adding Staff to the Penn+Box CNT Administration Folder
Adding Users to the ieeg.org Portal
Path BioResource Manager Access
Adding CAMRIS Users
Updating CAMRIS User Access
Onboarding & Offboarding
Onboarding & Offboarding
Onboarding & Offboarding Checklist
CNT Data & Computing Orientation
One HUP Pavilion Training
PennChart Training
Regulatory, IRB & Reporting
Regulatory, IRB & Reporting
Adding Personnel to an IRB Study
Adding a Non-Penn / New Hire to a Study
Closing an IRB Study
eDOA REDCap Entry
e-Regulatory Binder & eDoA (Audit Prep)
RPPR Demographic Tables
RPPR: Dates, Targets & Milestones
Consenting
Consenting
Consent Signing Checklist
3T Consent Script
7T Consent Script
All Consent Forms (Box links)
Consent Note Templates
How the e-Consent Form Works
Remote e-Consent Procedure
Scheduling Trackers
Scheduling Trackers
Scan Scheduling Trackers (sEEG, 3T/fMRI, 7T)
Archive: fMRI/3T Scans
Archive: 7T Scans
Archive: sEEG Implants
Participant Reimbursement (Greenphire)
Participant Reimbursement (Greenphire)
Greenphire ClinCard: Overview
Creating a Greenphire Account
Giving a User Study Access
Creating a New Study
Increasing a Study Budget
Ordering Physical Cards
Reimbursing a Participant
Postop Neuropsych Testing
Postop Neuropsych Testing
Postop Neuropsych Testing: Overview
Contacting & Scheduling Patients
Sending the Signed ICF & Attestation
Testing Battery
Running the Test
Scoring
Neuropsych Battery: Materials
Contacts
Contacts
Important Contacts & Emergency Numbers
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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