AFNI refers both to the interactive program of that name, and to the
entire software package. The basic unit of data storage is the "3D dataset",
which consists of one or more 3D arrays of voxel values (bytes,
shorts, floats, or complex numbers), plus some control information stored
in a header file.
Display of graphs (line and surface) of data extracted from image viewers.
Time series graphing of square regions from image viewers.
Linked image/graph viewing of multiple 3D datasets (e.g., linked scrolling
through multiple brains).
Transformation to Talairach coordinates (12 sub-volume piecewise linear method).
Computation of activation maps using the "correlation method".
Color overlay of activation maps onto higher-resolution anatomical images
(resampling of lower-resolution functionals is handled on the fly).
Interactive thresholding of functional overlays.
Command Line Programs
These programs are often used in batch processing scripts. They
take as input 3D AFNI datasets, and compute new 3D datasets as
output. The results can then be displayed or further processed
with the interactive AFNI program.
to3d -- Program to create a 3D AFNI dataset from image data.
3dmerge -- Program to average or otherwise merge multiple 3D datasets.
3dttest -- Program to do voxel-by-voxel t-tests on 3D datasets.
3dANOVA, 3dANOVA2, and 3dANOVA3 --
This series of program performs 1-way, 2-way, and 3-way
ANOVA tests across a collection of 3D datasets, on a
voxel-by-voxel basis.
3dRegAna -- Multiple linear regression across a collection of 3D datasets.
3dFriedman, 3dKruskalWallis, 3dMannWhitney, and 3dWilcoxon --
This series of programs carries out various nonparametric
statistical analyses across a collection of 3D datasets,
on a voxel-by-voxel basis.
3dDeconvolve -- Multiple linear regression of a 3D time series, including
linear deconvolution to find an ideal response vector
for each voxel.
3dNLfim -- Nonlinear regression of a 3D time series. The nonlinear
time series model functions can be anything programmable
in C.
Twelve sample model functions are supplied with the AFNI source code.
3dcalc -- General purpose 3D dataset calculator program.
3dTsmooth -- Program to smooth voxel time series.
3dfim -- Implements the "correlation method" on a 3D time series.
3dclust -- Program to find clusters of above-threshold voxels.
3dfractionize -- Program to resample an ROI mask from one grid spacing to another.
3dmaskave -- Program to compute statistics of voxels selected by an ROI mask.
3dpc -- Program to compute principal components from multiple 3D datasets.
3drotate -- Program to rotate the volumes in a 3D dataset.
2dImReg -- Program to do 2D (slice-wise) registration of a 3D time series.
3dvolreg -- Program to do 3D volume registration of a 3D time series.
3dTcat -- Utility program to catenate multiple 3D time series files into one.
3dbucket -- Utility program to catenate 3D volumes into one big "bucket".
3dbuc2fim -- Utility program to extract 3D volumes from a "bucket" dataset.
3dhistog -- Utility program to extract a histogram of a 3D dataset.
3dinfo -- Utility program to print out information about a 3D dataset.
3drefit -- Utility program to edit the header information about a 3D dataset.
3dTSgen -- Utility program to generate random 3D time series datasets from
nonlinear model equations; used for testing 3dNLfim and other
analysis codes.
AlphaSim -- Simulates noise-only 3D time series and activation detection
therefrom, in order to estimate the probability of false positives.
Used when analytical estimates for this p-value are unavailable.
adwarp -- Resample a functional dataset to the Talairach coordinate grid
defined by an anatomical "parent".
3daxialize -- Reorient the slices in a dataset to be in a standard
axial order.
3dIntracranial -- Remove the "scalp" from a T1-weighted high-resolution
anatomical dataset.
The following utility programs make certain tasks easier:
waver -- Utility program to generate an "ideal" response function for use
with the correlation method (or other regression analyses).
float_scan -- Utility program to scan a floating point file for illegal values (Infinity and NaN).
2swap,
4swap, and
24swap -- Utility programs to swap byte pairs
and quads; used when transferring data
between computers.
RSFgen -- Generates random stimulus timeseries
functions.
Interactive AFNI Plugins
Plugins are a way to add functionality to AFNI without modifying the
core software. There is a 40 page programming manual to aid in the
creation of new plugins.
plug_clust -- Interactive version of 3dclust.
plug_copy -- Make a copy of a dataset (useful for subsequent editing/drawing).
plug_deconvolve -- Interactive version of 3dDeconvolve.
plug_delay_V2 -- Hilbert transform estimation of time delay in active voxels.
plug_drawdset -- Draw values into a dataset (used to create ROI masks).
plug_edit -- Interactive version of 3dmerge
(voxel value editing functions).
plug_imreg -- 2D (slice-wise) image registration.
plug_lsqfit -- Interactive linear least squares regression on time series data.
plug_maskave -- Interactive version of 3dmaskave (statistics from an ROI).
plug_nlfit -- Interactive nonlinear least squares regression on time series data.
plug_power -- Power spectrum estimation from a 3D time series.
plug_realtime -- Real-time image acquisition, registration, and activation maps.
(Program rtfeedme is used to simulate real-time imaging, and
will transmit images into this plugin in lieu of a scanner.)
plug_render -- Volume rendering of 3D datasets, with color functional overlay.
plug_stats -- Compute some voxel-by-voxel statistics of a 3D time series.
plug_tag -- Put "tags" into a dataset, as markers for points of interest.
plug_volreg -- Interactive version of 3dvolreg (volume registration).
plug_reorder -- Reorder a 3D+time dataset; useful for
analysis of "event-related" FMRI data.