Reference manuals in PDF format. (Also available in postscript)
1dplot: Graph columns of *.1D type time series to screen
Graph columns of *.1D type time series to screen
24swap: Swaps byte pairs and/or quadruples on listed files
Swaps byte pairs and/or quadruples on listed files
2dImReg: Slice-by-slice image registration of FMRI 3D datasets
Slice-by-slice image registration of FMRIF 3D datasets
2swap: Swap byte pairs for inter-operating system compatibility
Swap byte pairs for inter-operating system compatibility
ANOVA: Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3
Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3 (updated Jan. 10, 2006)
3dbuc2fim: Convert bucket sub-bricks to fim (fico, etc.) datasets
Convert bucket sub-bricks to fim (fico, etc.) datasets
3dbucket: Concatenate individual sub-bricks into bucket dataset
Concatenate individual sub-bricks into bucket dataset
3dcalc: Do arithmetic on 3D datasets, voxel-by-voxel
Do arithmetic on 3D datasets, voxel-by-voxel
3dclust: Cluster detection and statistical summary
Cluster detection and statistical summary
3dDeconvolve: Deconvolution analysis of FMRI 3D time series data
Deconvolution analysis of FMRI 3D time series data (Updated January 24, 2006)
3ddup: Make duplicate copy of a 3D dataset
Make duplicate copy of a 3D dataset
3dfim: Cross correlation analysis of FMRI 3D time series data
Cross correlation analysis of FMRI 3D time series data
3dfim+
Program to calculate the cross-correlation of an ideal reference waveform with the measured FMRI time series for each voxel.
3dfractionize: Resample a mask dataset from a fine grid to a coarse grid
Resample a mask dataset from a fine grid to a coarse grid
3dFriedman: Nonparametric Friedman test for blocked multiple sample
Nonparametric Friedman test for blocked multiple sample
3dFWHM: Estimation of image Filter Width Half Maximum
Estimation of image Filter Width Half Maximum
3dinfo: Print out useful information from a 3D dataset header file
Print out useful information from a 3D dataset header file
3dIntracranial: Automatic segmentation of intracranial region
Automatic segmentation of intracranial region
3dKruskalWallis: Nonparametric Kruskal-Wallis test for multiple samples
Nonparametric Kruskal-Wallis test for multiple samples
3dMannWhitney: Nonparametric Mann-Whitney rank-sum two sample test
Nonparametric Mann-Whitney rank-sum two sample test
3dmaskave: Compute average of all voxels specified by a 3D mask
Compute average of all voxels specified by a 3D mask
3dmerge: Edit, cluster, filter, and merge FMRI 3D datasets
Edit, cluster, filter, and merge FMRI 3D datasets
3dnewid: Assign a new ID code to a dataset
Assign a new ID code to a dataset
3dNLfim Nonlinear Regression Analysis of FMRI time series data
Nonlinear Regression Analysis of FMRI time series data
3dnoise: Set voxels below noise threshold to zero
Set voxels below noise threshold to zero
3dnvals: Print out the number of sub-bricks in a 3D dataset
Print out the number of sub-bricks in a 3D dataset
3dpc: Principal Component Analyses of 3D datasets
Principal Component Analyses of 3D datasets
3dproject: Projection along cardinal axes from a 3D dataset
Projection along cardinal axes from a 3D dataset
3drefit: Change information in a 3D dataset's header
Change information in a 3D dataset's header
3dRegAna: Linear Regression Analysis of FMRI 3D datasets
Linear Regression Analysis of FMRI 3D datasets
3drotate: Rotate and/or translate all bricks from a 3D dataset
Rotate and/or translate all bricks from a 3D dataset
3dTcat: Concatenate sub-bricks into one 3D+time dataset
Concatenate sub-bricks into one 3D+time dataset
3dTSgen: Generates random signal+noice 3D datasets
Generates random signal+noice 3D datasets
3dTsmooth: Smooth each voxel time series in a 3D+time dataset
Smooth each voxel time series in a 3D+time dataset
3dttest: Perform t-test for sets of FMRI 3D datasets
Perform t-test for sets of FMRI 3D datasets
3dvolreg: Register each input 3D sub-brick to a base brick
Register each input 3D sub-brick to a base brick
3T_toafni: Send information about imaging sequence to AFNI
Send information about imaging sequence to AFNI
4swap: Swap byte quadruples on the files listed
Swap byte quadruples on the files listed
abut: Put noncontiguous FMRI slices together (for to3d)
Put noncontiguous FMRI slices together (for to3d)
adwarp: Resample dataset to grid defined by 'anat parent' dataset
Resample dataset to grid defined by 'anat parent' dataset
AlphaSim: Estimate statistical significance via Monte Carlo simulation
Estimate statistical significance via Monte Carlo simulation
byteorder: Indicates host CPU byte order
Indicates host CPU byte order
ccalc: Perform interactive arithmetic calculations
Perform interactive arithmetic calculations
cdf: Calculates various cumulative distribution probabilities
Calculates various cumulative distribution probabilities
count: Generates strings of numbers
Generates strings of numbers
FD2: Visualization of FMRI 2D dataset
Visualization of FMRI 2D datasets
fim2: Cross correlation analysis of FMRI 2D time series data
Cross correlation analysis of FMRI 2D time series data
float_scan: Scan input file of floating point numbers for illegal values
Scan input file of floating point numbers for illegal values
from3d: Extract 2D data files from 3D datasets
Extract 2D data files from 3D datasets
ftosh: Convert float 2D images to short 2D images
Convert float 2D images to short 2D images
imand: Produce logical "and" of a sequence of input images
Produce logical "and" of a sequence of input images
imaver: Compute mean and std. dev. of sequence of 2D images
Compute mean and std. dev. of sequence of 2D images
imcalc: Do arithmetic on 2D images, voxel-by-voxel
Do arithmetic on 2D images, voxel-by-voxel
imdump: Prints out non-zero pixels in a 2D image
Prints out non-zero pixels in a 2D image
immask: Apply mask to input 2D image
RSFgen: Generate random stimulus functions
Generate random stimulus functions
