AFNI

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AFNI

• Robert W Cox, PhD
• Scientific and Statistical Computing Core
• National Institute of Mental Health
• Bethesda, MD USA

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AFNI ? Analysis of Functional NeuroImages

• Philosophy
• Encompass all needed classes of data and
  computations
• Extensibility Openness Scalability Anticip
  ating 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 AFNI format datasets to3d
• Can be done at the scanner with the realtime
  plugin
• 3D 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
  plugin
• 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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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 many 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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Some Plugins

• plug_deconvolve - Interactive multiple linear
  regression
• plug_delay - Estimate delay of hemodynamic
  response
• plug_drawdset - Draw ROI masks (or other data)
• plug_histog - Graph histogram of dataset (or
  subregion)
• plug_nlfit - Interactive nonlinear time series
  regression
• plug_notes - Attach notes to a dataset
• plug_power - Power spectral density of time
  series
• plug_realtime - Read images from TCP/IP socket
• rtfeedme - Simulate realtime acquisition

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Volume Rendering Plugin
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Sample Rendering Coronal slice viewed from
side function not cut out
lt 0.5 CPU s per frame (Pentium III 800 MHz)
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Some More Batch Programs

• 3dIntracranial - Scalping T1-weighted volumes
• 3dWavelets - Daubechies decomposition of time
  series
• 3dcalc - General voxel-wise image calculator
• 3dclust - Find connected clusters of active
  voxels
• 3dmerge - Dataset editor and combiner
• 3drotate - Ill let you guess what this does
• 3dmaskdump - Dump voxel data to ASCII file
• 3dUndump - Take ASCII file and turn into
  dataset
• waver - Generate synthetic response to stimulus
  series

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Whole Brain Realtime FMRI

• Assembly of reconstructed images into AFNI
  datasets during acquisition
• Can use AFNI tools to visualize during scanning
• Everyone has realtime plugin - they just dont
  know it
• Realtime 3D registration
• Graph of estimated motion parameters
• What users say is most useful feature to have at
  scanner
• Recursive signal processing (linear regression)
  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
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Graph of Motion Params in Realtime
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Many Thanks To

• Doug Ward
• Andre Jesmanowicz
• Tom Ross
• Ziad Saad
• Mike Beauchamp
• Julie Bobholz and Julie Frost
• Malgorzata Klosek

and those who dare to ask quick questions