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TDT fMRI User Manual

Electrophysiology recording during functional mri
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fMRI User Guide
Electrophysiology recording during functional MRI
Updated 2021-01-28

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Summary of Contents for TDT fMRI

  • Page 1 User Guide Electrophysiology recording during functional MRI Updated 2021-01-28...
  • Page 2 The information contained in this document is provided "as is," and is subject to being changed, without notice. TDT shall not be liable for errors or damages in connection with the furnishing, use, or performance of this document or of any information contained herein.

  • Page 3: Table Of Contents

    Table of Contents | 3 Table of Contents fMRI User Guide Electrophyisology Recording in Functional MRI (fMRI) Environments using TDT Getting Started MRI Recording Processor Gizmo Physical Setup and Testing Troubleshooting FAQ Post Processing & Data Analysis...

  • Page 4: Fmri User Guide

    (LFP). The subject can be head- fixed or freely moving. In fMRI the subject is head-fixed and restrained in a tube. It measures changes in blood flow and relies on the fact that blood flow and neuronal activity are coupled. The activity is on a longer time scale, from several seconds to minutes.
  • Page 5 User Guide | 5 neural responses to stimulus, and elucidate the underlying neural activity driving the BOLD response.

  • Page 6: Getting Started

    (LP32CH-ZNF) form factors, with standard 2m cable. These headstages have a ±2.5V input range, unity gain, and no filters. For single unit / LFP recording, only fMRI-compatible probes can be used, with sites made of Platinum-Iridium (PtIr) or other materials. For EEG / EMG use non-ferrous materials that are also generally biocompatible.
  • Page 7 DC-coupled to minimize signal distortion. These are the only amplifiers that should be used with fMRI. Other amplifiers, including the digital headstages, have a much smaller input range and built-in filters. High-pass filters cause temporal shifts that make it more difficult for artifact removal.
  • Page 8 User Guide | 8 • (1) PA-DB25F, DB26 male to DB25 female connector • (1) PA-DB25M, DB26 female to DB25 male connector • (1) RFFILT-3M, RF filter with 50MHz low pass The MRI-NRKIT-32, 32 channel kit includes: • (2) PassThru •...
  • Page 9 Storage Drive that was provided with your shipment. Note *TDT drivers only function on Windows machines. Synapse will not run on Mac or Linux. Below is a list of helpful online TDT resources with which users should be familiar before starting: Synapse Training Videos Narrated walkthroughs of the Synapse software.
  • Page 10 Establishing RZ processor and PC communication Once the PO5e card is seated and TDT drivers and software are installed, you are ready to connect the RZ processor and PC together. The orange fiber optic cables* will be used for PC- RZ communication (see Sys III manual for more details).
  • Page 11 User Guide | 11 Connect your amplifier • If using a PZ5 and RZ2 processor, connect the PZ5 to the port labeled PZ Amplifier on the back of the RZ2. • If using a PZ5 and a different processor, connect it to the port labeled To PZ. On an RZ5D, this might be on the front panel.
  • Page 12 User Guide | 12 Note The PZ5 is unchecked because there isn't one connected. The Rig Editor can be accessed later for modification through the Synapse Menu if your hardware changes. Amplifier Setup SOFTWARE CONFIGURATION In Synapse, in the PZ5 or PZA Subject Interface options set the subamplifier to 'DC Coupled' mode.
  • Page 13 User Guide | 13 PZA configuration options The External Ground option connects the subamplifier / subject ground to the banana jack on the back of the PZ5 / PZA Subject Interface. Note that the subject ground should never be connected to the MRI ground.
  • Page 14 User Guide | 14 TOUCHSCREEN CONFIGURATION The amplifier produces high frequency EMF that is outside of any electrophysiological signal range, but is in the frequency range used by the scanner. This can introduce noise artifacts in the scanner image, as shown in the example below. These artifact show up as faint white lines across the image.
  • Page 15 User Guide | 15 PZA Subject Interface: Press the brightness icon on the touchscreen, this turns off the • touchscreen display after 5 seconds.

  • Page 16: Mri Recording Processor Gizmo

    User Guide | 16 MRI Recording Processor Gizmo Real-time Artifact Rejection The MRI Recording Processor gizmo is built into Synapse software. It provides a series of tools for thresholding and removing MRI scanner artifact in single unit and LFP data in real-time during the MRI recording.
  • Page 17 User Guide | 17 Note You can learn more about gizmos and experimental connections in the Synapse Manual. The MRI Recording Processor has several configuration options for managing how the artifact is detected and gated, and for which type of filtered waveform is output for other downstream processes.
  • Page 18 User Guide | 18 Important Enabling Plotting for Single Unit/LFP shows you the signals from all channels in the flow plot, but does not save the data. Storage gizmos, such as the Stream Data Storage, must be attached to the gizmo output link for saving.
  • Page 19 User Guide | 19 Example Run-Time View The MRI tab at run-time has the raw signal visualization and selected Single Unit and/or LFP plots. The amount of data is shows is set by the Working Window option during Idle. The gray vertical bar is the start of the artifact.
  • Page 20 User Guide | 20 You can also bypass the rejection to see the full scanner artifact and signal. This can help in setting up the appropriate rejection window and validating the artifact removal. Check Bypass on the upper right corner of the run-time interface.

  • Page 21: Physical Setup And Testing

    Subject Interface amp to the MRI. Any additional RF noise can be filtered with the passive low- pass 50MHz RF filter that comes with the TDT MRI-KIT. The RF filter is placed in-line between the amplifier and headstage. All wires (recording channels, subject ground, and reference) pass through this filter.
  • Page 22 DB25-female and DB25-male connectors provided in the TDT MRI kit to connect the headstage through the filter plate to the amplifier. Some filter plates are just pass-through connections, in which case you need to use the TDT RF filter in the cable connection.
  • Page 23 User Guide | 23 Minimizing Amplifier Artifact During MRI Scans We recommend the following setup: Place the PZ5 / PZA Subject Interface amplifier outside the MRI room in the control room or component room. You can place the amplifier on a cart in the control room just outside the penetration panel.
  • Page 24 User Guide | 24 Large Scanner Setups Scanners designed for humans and used for non-human primate (NHP) and large animals (pigs) are normally 3T and 7T large bore scanners. Large scanners are enclosed and do not have direct access to the MRI GND. Engineers are averse to providing access to GND lines that are accessible from the power and control room.
  • Page 25 The bore diameter will have a bigger effect. To do this: Perform test recordings with the 50k resistor block in the fMRI kit. This tests the integrity of the headstage / amplifier recording as a baseline. Run the system without a scan to observe the baseline noise.
  • Page 26 User Guide | 26 Run the system with a scan to view the scanner artifact on the neural recording. Look for any saturation, and use the MRI Recording Processor gizmo interface to remove the scanner artifact. View the scan to determine if there are any image artifacts.

  • Page 27: Troubleshooting Faq

    User Guide | 27 Troubleshooting FAQ Ringing still present Depending on the scanner artifact there could still be ringing in the Single Unit / LFP filters of the MRI Recording Processor gizmo after the artifact window has passed. In this case, only enable the Single Units artifact rejection and disable the built-in filters.
  • Page 28 User Guide | 28 Noise through filter plate If your MRI setup has a filter plate separating the control room and MRI room, the filter plate may have additional RF filtering. Sometimes the filter plate may slightly increase noise in the image. In that case, use a waveguide if available and the TDT RF filter.

  • Page 29: Post Processing & Data Analysis

    The TDT Python Package Data can also be easily imported into Python 3 using the tdt package. If you already have Python 3 installed, you can add the tdt package in your cmd window: pip install tdt Link to Python Package and SDK: https://pypi.org/project/tdt/...
  • Page 30 User Guide | 30 MATLAB and Python Workbook Examples TDT aims to help customers as much as possible with easy data import and analysis. We understand that not all customers have extensive MATLAB or Python experience, so we created fully-commented workbook examples that demonstrate how to do basic, but interesting operations with MATLAB or Python code.