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)

3dclust: Cluster detection and statistical summary

Cluster detection and statistical summary

3dcolon

 

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

3dExtrema

 

3dFDR

 

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

3dhistog

 

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

3dStatClust

 

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

3dWavelets

 

3dWilcoxon

 

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_fig

 

AlphaSim: Estimate statistical significance via Monte Carlo simulation

Estimate statistical significance via Monte Carlo simulation

buckets

 

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 datasets

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

 

imreg

 

imrotate

 

imstack

 

imstat

 

imupsam

 

mritopgm

 

Nonparametric

 

nsize

 

p2t

 

RSFgen: Generate random stimulus functions

Generate random stimulus functions

sfim

 

sqwave

 

Table

 

tfim

 

to3d

 

waver