AFNIAFNIRobert W Cox, PhDRobert W Cox, PhDBiophysics Research Institute

Medical College of Wisconsin

Milwaukee WI

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 Unix+X11+Motif (including Linux)

An FMRI Analysis Environment Philosophy:

Encompass all needed classes of data and computations Extensibility + Openness + Scalability:

Anticipating 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

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]

AFNI Controller Window

Interactive Analysis with AFNI

Graphing voxeltime series data

Displaying EP imagesfrom time series

ControlPanel

FIM overlaid on SPGR, in Talairach coords

Multislice layouts

Looking at the Results

Volume Rendering Controls

< 1 CPU s per frame(Pentium II 400 MHz)

SampleRendering:

Coronal sliceviewed from side;

function not cut out

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

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

Whole Brain Realtime FMRIWhole 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

The Goal: Interactive Functional Brain Mapping

See functional map as scanning proceeds

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