Wiki Category: Center equipment

Information about center equipment and resources for LCNI users.

Notes on FIRMM

Before registering a subject, run the “start FIRMM” batch file from the scanner console start menu. If you see “CONNECTED” you should be good to go.  If you see “NOT CONNECTED”, FIRMM will not work.

If you see “NOT CONNECTED”, run “stop FIRMM” from the console. Then restart the FIRMM tablet by pressing the power button. Note that it is possible to accidentally put the tablet into desktop mode. If that happens, just restart it again. FIRMM should launch and the tablet should say “not connected” and “please start a scan”. Now, run “start FIRMM” from the start menu again. This time there should be a “CONNECTED” message in the command window. Register your subject and FIRMM should work.

If you do this while a subject is already registered, you will need to close and re-register the subject before FIRMM will work again.

Mock Scanner

Our mock scanner is designed to provide participants an experience similar to what they will experience in the real scanner. It has a moving table, a realistic head coil, visual and audio stimulus capabilities and a set of button boxes for participant response. There is also a TR pulse simulator so you can trigger your stimulus programs just like the scanner would. Scheduling for the simulator is available in Calpendo.

Mock ScannerMock Scanner – Red arrow indicates location of the controls for moving the table.

Operation of the simulator table is done with a simple two-switch system, one to turn on the system, the other to move the table in and out. The location of these controls is indicated by the red arrow on the picture of the mock scanner, above.Table ControlsTable Controls – Power switch is on the left, in-out switch is on the right.

The table will automatically stop moving when it has reached the limits of its travel.

Visual stimuli are provided by an LG projector connected to a KVM switch. The switch is connected to a stimulus presentation computer on port two. Port one is available for your own laptop.

Projector and Controllers

Visual Stimulus – Provided by a small projector, switchable between two different video sources.

The switch controls the source video signal (DVI) delivered to the projector as well as the computer that receives the USB signal from the Psychology Software Tools button box system.

Audio simulating magnet noise is delivered by either the mac mini or your own computer. A power amplifier drives the simulator’s built-in speaker system.

It is important that your stimulus programs respond properly to the trigger pulse sent by the scanner. To test this, you can use our pulse simulator, a small black box located next to the projector. The green light indicates a powered on condition. Press the button indicated by the red arrow to generate the pulse.

TR Pulse Simulator

TR Pulse Simulator – Red arrow indicates the button used to generate a pulse.

Getting started at LCNI

Here are the steps to get a new project going at the center once you have completed safety training and have IRB approval for your study.

1. Get Research Compliance (IRB) approval. Send your approval notice to LCNI at lcni@uoregon.edu

2. Schedule R&D for your project, email LCNI at lcni@uoregon.edu

  • R&D worksheet: This will help us help you set up your protocol on the scanner. Bring this form to your R&D session with Vince and get it filled out. This will also help you estimate the resources you need when setting up your project in calpendo below. Email Diana to set up a time.

3. Set up Calpendo

  • If you do not have a Calpendo account, request one at the site
  • Go to Calpendo and create a new project under the Project menu. If you are unsure about how to answer fields in the Project menu, email us.

4. Start running your study

  • Schedule time through Calpendo. LCNI staff is available Monday-Friday 9a-5:30p. For after hours and weekend coverage details, email us at lcni@uoregon.edu.

5. Get access to dicoms

Collecting physiological data

It is possible to collect and record peripheral pulse, respiration, and electrocardiography data during any scan. In addition, two external trigger pulses may be recorded. The external trigger may be used to record the optical trigger out. This signal is currently available for BOLD echo-planar sequences and phosphorous spectroscopy, and may be added to other sequences if needed.

To record physiological signals, follow the instructions in the scanner operator manual. For peripheral pulse, simply place the pulse monitor on the subject’s fingertip, with the light facing the pad of the finger. Three sizes of transducer are available. The unit will begin measuring automatically and the results will be displayed in the monitor on the scanner.

To record the optical trigger, run a cable from the optical-to-digital converter box through the patch panel and into the external trigger in on the scanner. Alternatively, a second external trigger in is located in the equipment room.

Recording of physiological data files is initiated from the console and can be incorporated into any protocol. The files produced are text files, and begin with some header information and (for physiological signals) an average waveform. All signals have been resampled to 400 Hz, or a 2.5 ms sampling interval. Any detected triggers are marked with a value of 5000; these need to be removed from the file for accurate timing.

A command-line tool is available for converting these files to a more straightforward format is available to LCNI users. Currently it’s been compiled for Windows but can be recompiled for other platforms as needed.

This tool is run with the following options:

pmu_logfile_decoder filename [-t] [-r]

“filename” is the name of the logfiles, without extensions. The software will look for all matching logfiles in that location. The output files will have the additional extension “.out” and will consist of pairs of numbers: time in milliseconds and signal value, separated by a tab, with line breaks between pairs. Electrocardiogram signal files will be in groups of five: time, average, and individual channels.

The option -t indicates that all signals should be aligned with the external trigger in (currently this only works for the bay trigger, not ext2 located in the equipment room). All data before the first trigger signal and after the last trigger signal (plus the interval between triggers) is discarded for all signals. The option -r indicates that the “5000” trigger marks should be discarded. Both, either, or neither option may be chosen.

Auditory stimulus options

There are four options for auditory stimulus presentation and subject communication at LCNI: room intercom, the standard Siemens headphones, a set of headphones from Nordic Neurolabs (NNL), and a set of Sensimetrics earbuds. The right option for your project depends on which coils you are using and whether you are presenting auditory stimuli or simply communicating with the participant.

If you are using the 32-channel or 64-channel head coils, the options for stimulus presentation are the Sensimetrics earbuds or feeding audio into the room intercom. You may use the earbuds for stimulus presentation and the room intercom for subject communication.

If you are using prerecorded stimuli with the Sensimetrics earbuds, the sound quality will be greatly enhanced by prefiltering your sound files. Filtering software is available here: http://www.sens.com/products/model-s14/#downloads. You will also need the custom filter files for our earbuds; contact  for more information.

When using another head coil, or no head coil, we recommend either the Siemens or NNL headphones, as they will provide better sound insulation than the earbuds for most participants. For simple communication with the participant, the Siemens headphones will suffice. If you are presenting auditory stimuli, you should use the NNL headphones.

For participant-to-operator communications, you may use either the room intercom or the Persaio MR noise cancelling audio system.