1. AFNI Robert W Cox, PhD Biophysics Research Institute Medical College of Wisconsin Milwaukee WI

2. 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)

3. 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

4. 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]

5. AFNI Controller Window

6. Interactive Analysis with AFNI Graphing voxel time series data Displaying EP images from time series Control Panel

7. FIM overlaid on SPGR, in Talairach coordsMultislice layouts Looking at the Results

8. Volume Rendering Controls

9. < 1 CPU s per frame (Pentium II 400 MHz) Sample Rendering: Coronal slice viewed from side; function not cut out

10. 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

11. 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

12. 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

13. The Goal: Interactive Functional Brain Mapping  See functional map as scanning proceeds 1 minute 2 minutes 3 minutes