Getting Started at CFMRI

• Getting Started at CFMRI
  • Conducting Research at the CFMRI - 3T Scanners
    • 1. Contact CFMRI
    • 2. Create a Project
    • 3. Proposal Approval
    • 4. Safety Training
    • 5. Operator Training
    • 6. CFMRI Building Access and Scanner Access
    • 7. Join Our Mailing Lists

Center Policies

• Center Policies
  • Scanning
    • Policies for Using the 3T Scanner
    • Center Locker Policies
    • Guidelines for Clinical Evaluation of Research MRI Studies
  • Safety
    • Safety Manual for Using the Scanner
    • Supplementary Safety Guidelines
  • Short-Duration Workspace
    • Short-Duration Workspace Policy
  • Parking
    • Parking Policy
  • Computing Resources
    • UCSD Center for Functional MRI Computing Resources and Usage Statement

CFMRI Siemens Prisma User Documentation

• CFMRI Siemens Prisma User Documentation

Training

• Training
  • Safety Training
  • Operator Training

Safety

• Safety
  • Emergency Power Shutoff
  • Quenching the Scanner
  • Gauss Lines
  • Fire Extinguisher
  • Safety Documentation

COVID-19 Operational Updates-CFMRI

• COVID-19 Operational Updates-CFMRI
  • CFMRI-UCSD Updated COVID Policies Effective 04/14/23
    • Masking During the MRI Scan
    • Sanitization Protocols
    • COVID Screening for Research Volunteers
    • COVID-19: UCSD Center for fMRI Operational Updates
    • Additional COVID-19 Information

fMRI Seminar Series 2019-2020

• Upcoming Virtual Seminar Details
• Previous Seminars
  • Meher Juttukonda, Ph.D. - 10/12/21: 12:00 pm
    • Imaging cerebral hemodynamics in typical and abnormal aging
  • Frederik Laun, Ph.D. - 02/23/21: 12:00 pm
    • Diffusion-weighted imaging of the liver and breast – and on its inverse problem
  • Moritz Zaiss, Ph.D. - 01/12/21: 12:00 pm
    • CEST MRI – basics, tricks and applications
  • Jean Chen, Ph.D. - 07/28/20: 10:00 -11:00 am
    • Mapping age effects on functional and structural connectivity in aging: Physiological considerations
  • Jia Guo - 03/11/20: 1:00 pm
    • “Faster, higher, stronger”: arterial spin labeling as a non-invasive tool for perfusion mapping
  • Jiang Du - 03/03/20: 12:00 pm
    • Ultrashort Echo Time Magnetic Resonance Imaging of Myelin
  • Martin Sereno - 02/18/20: 12:00 pm
    • DNA and Language: Origin vs. Evolution of Symbol-Using Systems
  • Selda Yildiz - 02/07/20: 12:00 pm
    • Yogic Breathing, Sleep, and Non-Invasive MRI-Based Measures of Cerebrospinal Fluid Circulation
  • Rick Buxton - 01/14/20: 12:00 pm
    • The thermodynamics of thinking: connections between neural activity, energy metabolism and blood flow
  • Christine Fennema-Notestine - 12/3/19: 12:00 pm
    • Multi-channel structural MRI measures of white matter disease: Associations with immune recovery, inflammation, hypertension, and cognition in HIV and Aging
  • Gadi Goelman - 10/21/19: 4:00 pm
    • Multivariate functional connectivity analysis to obtain directed pathways of multiple-nodes
  • Eric Wong - 11/12/19: 12:00 pm
    • Example-based Hebbian learning: from prediction to complex thought

Imaging Protocol Documentation

• CFMRI GE MR750 Imaging Protocol Documentation
  • CFMRI Multiband Protocol #1
    • Protocol Location and Receiver Coil Info
    • Pre-Scan Preparation
    • Data Acquisition: EPI & Topup Distortion Correction
    • Data Acquisition: Diffusion Tensor Imaging (DTI)
    • DTI Distortion Correction Acquisition Option #1:
    • DTI Distortion Correction Acquisition Option #2:
  • CFMRI Multiband Protocol #2
    • Protocol Location and Receiver Coil Info
    • Pre-Scan Preparation
    • Data Acquisition: EPI & Topup Distortion Correction
  • Diffusion Tensor Imaging User Guide
    • Introduction
    • Protocol #1
    • Protocol #2
    • Protocol #3
    • DTI TOPUP Distortion Correction
  • Arterial Spin Labeling User Guide
    • Background
    • ASL FAQs
    • What is ASL?
    • What types of ASL are available at CFMRI?
    • What is new in ASL at CFMRI?
    • Where do I find the updated CFMRI ASL protocols?
    • 2D PCASL Protocol Coverage
    • 3D PCASL Protocol Coverage
    • FAIR Protocol Coverage
    • How do I transfer data acquired from the scanner?
    • Between FAIR and PCASL, which one should I use?
    • Between 2D PCASL and 3DPCASL, which one should I use?
    • What are the standard scan and labeling parameters for each protocol?
    • What other ASL techniques are out there?
    • References

Multiband Data Management

• Navigating & Interacting with Multiband Data Effectively at CFMRI
  • Automated Multiband Reconstruction Process
  • Basic Description of the Multiband Reconstruction Process
  • What You Need to Know as a Scanner Operator
  • Instructions for Viewing and Pulling Data from AWS
    • To view available files from CFMRI AWS buckets
    • To copy a file to your current directory
    • To search specifically for your scan files
    • To copy all your reconstructed nii.gz files
  • Auto-Recon Failures
    • Manually reconstructing your data on fmri1, fmri2, or fmri3
  • Z-Stretched Reconstructions
    • Why does this happen?
    • What does it look like?
    • How do I fix it?

3T Scanner Troubleshooting Guide

• 3T Troubleshooting Guide
  • Weight out of Range Error
    • Symptoms
    • Solution

3T Audio System Usage

• Audio Stimulus Presentation at CFMRI
  • Troubleshooting Audio Issues
    • Console Room Connections
    • Magnet Room Connections

Post-Scan Data Transfer

• Post-Scan Data Transfer
  • cfmricp
  • Using cfmricp Across Multiple Back-to-Back Scan Sessions

Imaging Data Analysis

• Imaging Data Analysis & QA
  • Plotting Motion Across an Imaging Run
  • Brief Overview of Multiband Acquisition
  • Distortion Correction at CFMRI
    • fMRI Topup at CFMRI

Intro to Terminal/Command Prompt Usage

• Intro to Terminal/Command Prompt Usage
  • Common commands used when working in terminal/linux based systems

CFMRI BIDS conversion script cfmridcm2bids

• CFMRI BIDS conversion script cfmridcm2bids
  • About the cfmridcm2bids
  • Prerequisites for using cfmridcm2bids
  • Start the cfmridcm2bids
    • Step 1 - start the script
    • Step 2 - select the input and output folders
    • Step 3 - enter subject and session info
    • Step 4 - create the BIDS configuration file
    • Step 5 - transfer the data
    • Step 6 - sanity checks on the data after conversion
  • Questions and suggestions
  • Useful links

Removing ID Info from Dicom Data

• FMRIVAST Dicom Data Anonymization
  • Dicom Date Stripping Prior to Transfer to fmrivast.ucsd.edu
    • cfmricp_log.txt
    • Dicom Date Stripping

CBFBIRN Processing

• CBFBIRN Processing
  • Code Flow
  • Understanding Your Files
  • Subject Setup Script
  • Constructing Initial BRIKs and Fieldmap Correction - dofmapGEN
  • Quantifying CBF - processASLGEN2
  • Reference - Table of Outputs

Peripheral Equipment Usage

• Peripheral Equipment Usage
  • Projectors
  • Button Boxes

Neuroimaging Software Installation Guides

• Imaging Software Installation
  • Analysis of Functional Neuroimages (AFNI)
  • FSL: FMRIB Software Library
  • FreeSurfer Software Suite
  • MATLAB
    • Create a mathorks account at https://www.mathworks.com/ using your UCSD email address
    • Link to the UCSD license (if you are not connected to it by default)
    • The UCSD license should be listed as 1144083
    • Click on the “products” tab at the top of your account page
    • Download the latest release after providing your OS info
    • Unzip the downloaded file
    • Open the disk image
    • Run the installer
    • Log in using your Mathworks account credentials
    • Accept the license agreement
    • Select the campus license
    • Choose the install location (Applications or default is OK)
    • Select the products to install
    • Install Matlab

Alternative Parking Options

• Alternative Parking Options
  • Special Event Parking
  • Parkmobile Promo Codes
  • Free 30-Minute Visitor Parking
  • Parkmobile Download

Additional Info

• Contact Info & Directions
  • Mailing Address
  • Directions
• Need Assistance?
  • Need further help

Indices and tables

• Index

• Module Index

• Search Page