Reference Manuals
Up one levelReference manuals in PDF format. (Also available in postscript)
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1dplot: Graph columns of *.1D type time series to screen
- Graph columns of *.1D type time series to screen
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24swap: Swaps byte pairs and/or quadruples on listed files
- Swaps byte pairs and/or quadruples on listed files
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2dImReg: Slice-by-slice image registration of FMRI 3D datasets
- Slice-by-slice image registration of FMRIF 3D datasets
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2swap: Swap byte pairs for inter-operating system compatibility
- Swap byte pairs for inter-operating system compatibility
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ANOVA: Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3
- Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3 (updated Jan. 10, 2006)
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3daxialize
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3dbuc2fim: Convert bucket sub-bricks to fim (fico, etc.) datasets
- Convert bucket sub-bricks to fim (fico, etc.) datasets
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3dbucket: Concatenate individual sub-bricks into bucket dataset
- Concatenate individual sub-bricks into bucket dataset
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3dcalc: Do arithmetic on 3D datasets, voxel-by-voxel
- Do arithmetic on 3D datasets, voxel-by-voxel
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3dclust: Cluster detection and statistical summary
- Cluster detection and statistical summary
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3dcolon
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3dDeconvolve: Deconvolution analysis of FMRI 3D time series data
- Deconvolution analysis of FMRI 3D time series data (Updated January 24, 2006)
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3ddup: Make duplicate copy of a 3D dataset
- Make duplicate copy of a 3D dataset
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3dExtrema
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3dFDR
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3dfim: Cross correlation analysis of FMRI 3D time series data
- Cross correlation analysis of FMRI 3D time series data
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3dfim+
- Program to calculate the cross-correlation of an ideal reference waveform with the measured FMRI time series for each voxel.
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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
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3dFriedman: Nonparametric Friedman test for blocked multiple sample
- Nonparametric Friedman test for blocked multiple sample
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3dFWHM: Estimation of image Filter Width Half Maximum
- Estimation of image Filter Width Half Maximum
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3dhistog
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3dinfo: Print out useful information from a 3D dataset header file
- Print out useful information from a 3D dataset header file
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3dIntracranial: Automatic segmentation of intracranial region
- Automatic segmentation of intracranial region
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3dKruskalWallis: Nonparametric Kruskal-Wallis test for multiple samples
- Nonparametric Kruskal-Wallis test for multiple samples
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3dMannWhitney: Nonparametric Mann-Whitney rank-sum two sample test
- Nonparametric Mann-Whitney rank-sum two sample test
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3dmaskave: Compute average of all voxels specified by a 3D mask
- Compute average of all voxels specified by a 3D mask
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3dmerge: Edit, cluster, filter, and merge FMRI 3D datasets
- Edit, cluster, filter, and merge FMRI 3D datasets
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3dnewid: Assign a new ID code to a dataset
- Assign a new ID code to a dataset
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3dNLfim Nonlinear Regression Analysis of FMRI time series data
- Nonlinear Regression Analysis of FMRI time series data
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3dnoise: Set voxels below noise threshold to zero
- Set voxels below noise threshold to zero
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3dnvals: Print out the number of sub-bricks in a 3D dataset
- Print out the number of sub-bricks in a 3D dataset
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3dpc: Principal Component Analyses of 3D datasets
- Principal Component Analyses of 3D datasets
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3dproject: Projection along cardinal axes from a 3D dataset
- Projection along cardinal axes from a 3D dataset
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3drefit: Change information in a 3D dataset's header
- Change information in a 3D dataset's header
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3dRegAna: Linear Regression Analysis of FMRI 3D datasets
- Linear Regression Analysis of FMRI 3D datasets
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3drotate: Rotate and/or translate all bricks from a 3D dataset
- Rotate and/or translate all bricks from a 3D dataset
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3dStatClust
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3dTcat: Concatenate sub-bricks into one 3D+time dataset
- Concatenate sub-bricks into one 3D+time dataset
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3dTSgen: Generates random signal+noice 3D datasets
- Generates random signal+noice 3D datasets
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3dTsmooth: Smooth each voxel time series in a 3D+time dataset
- Smooth each voxel time series in a 3D+time dataset
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3dttest: Perform t-test for sets of FMRI 3D datasets
- Perform t-test for sets of FMRI 3D datasets
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3dvolreg: Register each input 3D sub-brick to a base brick
- Register each input 3D sub-brick to a base brick
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3dWavelets
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3dWilcoxon
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3T_toafni: Send information about imaging sequence to AFNI
- Send information about imaging sequence to AFNI
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4swap: Swap byte quadruples on the files listed
- Swap byte quadruples on the files listed
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abut: Put noncontiguous FMRI slices together (for to3d)
- Put noncontiguous FMRI slices together (for to3d)
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adwarp: Resample dataset to grid defined by 'anat parent' dataset
- Resample dataset to grid defined by 'anat parent' dataset
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AlphaSim_fig
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AlphaSim: Estimate statistical significance via Monte Carlo simulation
- Estimate statistical significance via Monte Carlo simulation
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buckets
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byteorder: Indicates host CPU byte order
- Indicates host CPU byte order
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ccalc: Perform interactive arithmetic calculations
- Perform interactive arithmetic calculations
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cdf: Calculates various cumulative distribution probabilities
- Calculates various cumulative distribution probabilities
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count: Generates strings of numbers
- Generates strings of numbers
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FD2: Visualization of FMRI 2D datasets
- Visualization of FMRI 2D datasets
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fim2: Cross correlation analysis of FMRI 2D time series data
- Cross correlation analysis of FMRI 2D time series data
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float_scan: Scan input file of floating point numbers for illegal values
- Scan input file of floating point numbers for illegal values
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from3d: Extract 2D data files from 3D datasets
- Extract 2D data files from 3D datasets
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ftosh: Convert float 2D images to short 2D images
- Convert float 2D images to short 2D images
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imand: Produce logical "and" of a sequence of input images
- Produce logical "and" of a sequence of input images
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imaver: Compute mean and std. dev. of sequence of 2D images
- Compute mean and std. dev. of sequence of 2D images
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imcalc: Do arithmetic on 2D images, voxel-by-voxel
- Do arithmetic on 2D images, voxel-by-voxel
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imdump: Prints out non-zero pixels in a 2D image
- Prints out non-zero pixels in a 2D image
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immask: Apply mask to input 2D image
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imreg
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imrotate
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imstack
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imstat
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imupsam
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mritopgm
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Nonparametric
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nsize
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p2t
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RSFgen: Generate random stimulus functions
- Generate random stimulus functions
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sfim
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sqwave
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Table
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tfim
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to3d
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waver