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Reference Manuals

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Reference manuals in PDF format. (Also available in postscript)
Reference Manuals ANOVA: Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3
Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3 (updated Jan. 10, 2006)
Reference Manuals 3dclust: Cluster detection and statistical summary
Cluster detection and statistical summary
Reference Manuals 3dcolon
 
Reference Manuals 3dDeconvolve: Deconvolution analysis of FMRI 3D time series data
Deconvolution analysis of FMRI 3D time series data (Updated January 24, 2006)
Reference Manuals 3ddup: Make duplicate copy of a 3D dataset
Make duplicate copy of a 3D dataset
Reference Manuals 3dExtrema
 
Reference Manuals 3dFDR
 
Reference Manuals 3dfim: Cross correlation analysis of FMRI 3D time series data
Cross correlation analysis of FMRI 3D time series data
Reference Manuals 3dfim+
Program to calculate the cross-correlation of an ideal reference waveform with the measured FMRI time series for each voxel.
Reference Manuals 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
Reference Manuals 3dFriedman: Nonparametric Friedman test for blocked multiple sample
Nonparametric Friedman test for blocked multiple sample
Reference Manuals 3dFWHM: Estimation of image Filter Width Half Maximum
Estimation of image Filter Width Half Maximum
Reference Manuals 3dhistog
 
Reference Manuals 3dinfo: Print out useful information from a 3D dataset header file
Print out useful information from a 3D dataset header file
Reference Manuals 3dIntracranial: Automatic segmentation of intracranial region
Automatic segmentation of intracranial region
Reference Manuals 3dKruskalWallis: Nonparametric Kruskal-Wallis test for multiple samples
Nonparametric Kruskal-Wallis test for multiple samples
Reference Manuals 3dMannWhitney: Nonparametric Mann-Whitney rank-sum two sample test
Nonparametric Mann-Whitney rank-sum two sample test
Reference Manuals 3dmaskave: Compute average of all voxels specified by a 3D mask
Compute average of all voxels specified by a 3D mask
Reference Manuals 3dmerge: Edit, cluster, filter, and merge FMRI 3D datasets
Edit, cluster, filter, and merge FMRI 3D datasets
Reference Manuals 3dnewid: Assign a new ID code to a dataset
Assign a new ID code to a dataset
Reference Manuals 3dNLfim Nonlinear Regression Analysis of FMRI time series data
Nonlinear Regression Analysis of FMRI time series data
Reference Manuals 3dnoise: Set voxels below noise threshold to zero
Set voxels below noise threshold to zero
Reference Manuals 3dnvals: Print out the number of sub-bricks in a 3D dataset
Print out the number of sub-bricks in a 3D dataset
Reference Manuals 3dpc: Principal Component Analyses of 3D datasets
Principal Component Analyses of 3D datasets
Reference Manuals 3dproject: Projection along cardinal axes from a 3D dataset
Projection along cardinal axes from a 3D dataset
Reference Manuals 3drefit: Change information in a 3D dataset's header
Change information in a 3D dataset's header
Reference Manuals 3dRegAna: Linear Regression Analysis of FMRI 3D datasets
Linear Regression Analysis of FMRI 3D datasets
Reference Manuals 3drotate: Rotate and/or translate all bricks from a 3D dataset
Rotate and/or translate all bricks from a 3D dataset
Reference Manuals 3dStatClust
 
Reference Manuals 3dTcat: Concatenate sub-bricks into one 3D+time dataset
Concatenate sub-bricks into one 3D+time dataset
Reference Manuals 3dTSgen: Generates random signal+noice 3D datasets
Generates random signal+noice 3D datasets
Reference Manuals 3dTsmooth: Smooth each voxel time series in a 3D+time dataset
Smooth each voxel time series in a 3D+time dataset
Reference Manuals 3dttest: Perform t-test for sets of FMRI 3D datasets
Perform t-test for sets of FMRI 3D datasets
Reference Manuals 3dvolreg: Register each input 3D sub-brick to a base brick
Register each input 3D sub-brick to a base brick
Reference Manuals 3dWavelets
 
Reference Manuals 3dWilcoxon
 
Reference Manuals 3T_toafni: Send information about imaging sequence to AFNI
Send information about imaging sequence to AFNI
Reference Manuals 4swap: Swap byte quadruples on the files listed
Swap byte quadruples on the files listed
Reference Manuals abut: Put noncontiguous FMRI slices together (for to3d)
Put noncontiguous FMRI slices together (for to3d)
Reference Manuals adwarp: Resample dataset to grid defined by 'anat parent' dataset
Resample dataset to grid defined by 'anat parent' dataset
Reference Manuals AlphaSim_fig
 
Reference Manuals AlphaSim: Estimate statistical significance via Monte Carlo simulation
Estimate statistical significance via Monte Carlo simulation
Reference Manuals buckets
 
Reference Manuals byteorder: Indicates host CPU byte order
Indicates host CPU byte order
Reference Manuals ccalc: Perform interactive arithmetic calculations
Perform interactive arithmetic calculations
Reference Manuals cdf: Calculates various cumulative distribution probabilities
Calculates various cumulative distribution probabilities
Reference Manuals count: Generates strings of numbers
Generates strings of numbers
Reference Manuals FD2: Visualization of FMRI 2D datasets
Visualization of FMRI 2D datasets
Reference Manuals fim2: Cross correlation analysis of FMRI 2D time series data
Cross correlation analysis of FMRI 2D time series data
Reference Manuals float_scan: Scan input file of floating point numbers for illegal values
Scan input file of floating point numbers for illegal values
Reference Manuals from3d: Extract 2D data files from 3D datasets
Extract 2D data files from 3D datasets
Reference Manuals ftosh: Convert float 2D images to short 2D images
Convert float 2D images to short 2D images
Reference Manuals imand: Produce logical "and" of a sequence of input images
Produce logical "and" of a sequence of input images
Reference Manuals imaver: Compute mean and std. dev. of sequence of 2D images
Compute mean and std. dev. of sequence of 2D images
Reference Manuals imcalc: Do arithmetic on 2D images, voxel-by-voxel
Do arithmetic on 2D images, voxel-by-voxel
Reference Manuals imdump: Prints out non-zero pixels in a 2D image
Prints out non-zero pixels in a 2D image
Reference Manuals immask: Apply mask to input 2D image
 
Reference Manuals imreg
 
Reference Manuals imrotate
 
Reference Manuals imstack
 
Reference Manuals imstat
 
Reference Manuals imupsam
 
Reference Manuals mritopgm
 
Reference Manuals Nonparametric
 
Reference Manuals nsize
 
Reference Manuals p2t
 
Reference Manuals RSFgen: Generate random stimulus functions
Generate random stimulus functions
Reference Manuals sfim
 
Reference Manuals sqwave
 
Reference Manuals Table
 
Reference Manuals tfim
 
Reference Manuals to3d
 
Reference Manuals waver
 
 

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