MoTrakĀ®, Realtime AFNI, and FIRMM

Keep On Truckin

How to Watch Subject Motion in Realtime

Nate Vack
Dan Fitch
John Koger
CHM Research Support Core, BI Core


What it does

  • Trains participants in the simulator
  • Strap sensor to participant forehead
  • They see visual feedback on the screen
  • Experimenter can talk them through it
MoTrak screenshot

Realtime AFNI

What it does

  • Runs AFNI motion correction in realtime
  • Shows you 6-degree-of-freedom motion plots
AFNI plot

Why you might care

  • You know if you need to tell your participant to stop wiggling
  • ... or if they're a lost cause and you can stop scanning them


  • This is not how to properly do motion correction
  • We don't save the results for you


Framewise Integrated Realtime MRI Monitoring

What it does

  • Simple framewise displacement (FD) graphs
  • Customizable thresholds
  • Resting state "known good" time prediction
FIRMM screenshot


  • GE testing site
  • Fast TRs = no longer always realtime

How DICOM images get from the scanner to useful places (Basic)

  • We copy images from the scanner console a processing computer
  • The processing computer does... processing
  • We use another computer for display

Why do we do this complicated thing?

  • The software running on the scanner is very simple
  • The processing host can do its job without affecting the scanner
  • The processing computer and display computer are in different rooms

How images get from the scanner to useful places (Advanced)

  • The scanner uses NFS to connect to the processing computer
  • The scanner runs a script that watches for new DICOMs and copies them to the processing computer
  • This script looks at the pulse sequence name and only copies fMRI DICOMs

How DICOM images get from the scanner to useful places (Advanced)

  • The display computer connects to the processing computer via SSH and runs a script
  • This script watches the target directory for new DICOMs
  • When it finds one, it starts Realtime AFNI
  • When that ends, it tries to clean up the files that got created
  • Once a day, old files get purged

Source code is available!

Why should you care?

  • We're doing realtime motion information
  • ... but you can do whatever you want
  • Biofeedback fMRI? Something even cooler?
  • You just need to be able to handle a stream of DICOM images
  • Get in touch if you want to try