AFNI

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AFNI

• Robert W Cox, PhD
• Biophysics Research Institute
• Medical College of Wisconsin
• Milwaukee WI

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AFNI ? Analysis of Functional NeuroImages

• Genesis (mid-1994) Need for MCW
  neuroscientists to transform FMRI activation maps
  to Talairach-Tournoux coordinates
• Initial goals
• T-T transformation via manual AC-PC marking
• Interactive browsing of image data in 5
  dimensions 3 spatial imaging run subject
• Basic unit of data 3D AFNI dataset
• Big array of numbers plus geometrical
  information
• Developed for UnixX11Motif (including Linux)

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An FMRI Analysis Environment

• Philosophy
• Encompass all needed classes of data and
  computations
• Extensibility Openness Scalability Antici
  pating what will be needed to solve problems that
  have not yet been posed
• Interactive vs. Batch operations Stay close
  to data or view from a distance
• Components
• Data Objects Arrays of 3D arrays
  auxiliary data
• Data Viewers Numbers, Graphs, Slices,
  Volumes
• Data Processors Plugins, Plugouts, Batch
  Programs

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Steps in Processing with AFNI

• Image assembly into datasets to3d
• Can be done at the scanner with the realtime
  plugin
• Image registration 3dvolreg
• Functional activation calculations AFNI, 3dfim
• Linear and nonlinear time series regression
  3dDeconvolve, 3dNLfim
• Transformation to Talairach coordinates AFNI
• Alternative selection of anatomical ROIs AFNI
  
• Integration of results from multiple subjects
  many
• Visualization of thinking about results AFNI
  you

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AFNI Controller Window
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Interactive Analysis with AFNI
Control Panel
Graphing voxel time series data
Displaying EP images from time series
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Looking at the Results
FIM overlaid on SPGR, in Talairach coords
Multislice layouts
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Volume Rendering Controls
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Sample Rendering Coronal slice viewed from
side function not cut out
lt 1 CPU s per frame (Pentium II 400 MHz)
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Integration of Results

• Done with batch programs (usually in scripts)
• 3dmerge edit and combine 3D datasets
• 3dttest voxel-by-voxel 1- and 2-sample t-tests
• 3dANOVA
• Voxel-by-voxel 1-, 2-, and 3-way layouts
• Fixed and random effects
• Other voxel-by-voxel statistics are available
• 3dpc principal components (space ? time)
• ROI analyses are a labor-intensive alternative

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Extending AFNI Package

• Batch programs
• Output new 3D datasets for viewing with AFNI
• Plugins searched for and loaded at startup
• Add interactive capabilities to AFNI program
• Fill in the blanks menu for input from users
• 40 page manual and some samples included
• Plugouts attach themselves in middle of run
• External programs that communicate with AFNI
  with shared memory or TCP/IP sockets

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Whole Brain Realtime FMRI

• Assembly of images into AFNI datasets during
  acquisition
• Can use AFNI tools to visualize during scanning
• Realtime 3D registration
• Graph of estimated motion parameters
• Recursive signal processing to update activation
  map with each new data volume
• Color overlay changes with each TR

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The Goal Interactive Functional Brain Mapping

• See functional map as scanning proceeds

1 minute 2 minutes
3 minutes