AFNI and NIfTI Server for NIMH/NIH/PHS/DHHS/USA/Earth

HowTo 00 : Installing AFNI

aclark — 2009-03-17 17:59:23

Installing AFNI

afni

aclark — 2008-04-23 11:11:24

afni

Advanced 3dDeconvolve

bpittman — 2008-03-19 17:41:46

Advanced 3dDeconvolve

AFNI Deconvolution

bpittman — 2008-03-19 17:39:19

AFNI Deconvolution

AFNI Regression

bpittman — 2008-03-19 17:37:14

AFNI Regression

AFNI FMRI

bpittman — 2008-03-19 17:35:07

AFNI FMRI

AFNI Soup to Nuts

aclark — 2008-03-19 17:29:01

AFNI Soup to Nuts

3dFWHM: Usage: 3dFWHM -dset dataset

aclark — 2007-10-02 18:08:25

Volume Registration and Talairach Transform

aclark — 2007-05-09 15:17:59

Volume Registration and the Talairach Transformation

Basis Function Suggestions

rickr — 2007-05-07 10:29:56

Suggested Choices for Basis Functions for use with -stim_times in 3Ddeconvolve

Notes on Parallelizing AFNI Programs (3dDeconvolve On FreeBSD)

aclark — 2007-04-19 10:53:15

Notes on increasing the shared memory limit on FreeBSD 5.x by Jason Bacon

Experiment Design

aclark — 2007-04-18 16:26:11

Experiment Design

class data

aclark — 2007-04-02 14:53:53

all AFNI data: directory tree for AFNI class data

class handouts: latest tree

rickr — 2007-04-02 14:53:20

all AFNI handouts: directory tree for latest handouts

3dDeconvolve Upgrades - Summer 2004

aclark — 2007-03-14 14:02:13

3dDeconvolve Upgrades

3dDeconvolve Changes - Spring 2007

rwcox — 2007-03-14 13:58:15

Several Small Things, and One Big Thing

Using AFNI Interactively

aclark — 2006-09-28 12:19:02

A tour of the main AFNI graphical interface

Unix Essentials

aclark — 2006-09-28 12:17:48

An introduction to UNIX

AFNI Jazzercize

christip — 2006-09-28 12:16:13

An exercise in using various AFNI programs, plugins, and the main AFNI interface.

Show me the Anterior and Posterior commissures!

rwcox — 2006-06-28 10:20:07

How do I register data from the same subject taken on different days?

rwcox — 2006-06-07 15:38:35

1ddot: Usage: 1ddot [options] 1Dfile 1Dfile ...

aclark — 2006-04-13 15:07:35

1dcat: Usage: 1dcat a.1D b.1D ...

aclark — 2006-04-13 15:06:34

Attributes in the AFNI Dataset Header

aclark — 2006-04-13 14:27:58

Attributes in the AFNI Dataset Header

3dFDR: Usage: 3dFDR [options] dataset

aclark — 2006-03-17 21:23:41

3dpc: Principal Component Analyses of 3D datasets

aclark — 2006-02-23 16:06:03

Principal Component Analyses of 3D datasets

3dDeconvolve: Deconvolution analysis of FMRI 3D time series data

aclark — 2006-01-24 15:07:25

Deconvolution analysis of FMRI 3D time series data (Updated January 24, 2006)

3dRegAna: Linear Regression Analysis of FMRI 3D datasets

aclark — 2006-01-24 14:01:26

Linear Regression Analysis of FMRI 3D datasets

ANOVA: Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3

aclark — 2006-01-17 11:53:17

Manual for three ANOVA programs: 3dANOVA, 3dANOVA2, and 3dANOVA3 (updated Jan. 10, 2006)

NIML Documentation

rwcox — 2006-01-05 11:55:10

Documentation of the NIML format and C API (such as it is).

Classroom Setup

aclark — 2005-09-01 11:27:27

Details of classroom setup. Largely based on the experiences of the SSCC in AFNI Bootcamp.

3dDeconvolve Speed Test

aclark — 2005-09-01 11:26:58

3dDeconvolve Speed Test

An evaluation of thresholding techniques in fMRI analysis

aclark — 2005-08-30 15:43:46

An evaluation of thresholding techniques in fMRI analysis

FDR

aclark — 2005-08-30 15:30:19

False Discovery Rate (Benjamini & Hochberg, 1995) is a relatively new statistical procedure that controls the number of mistakes make when performing multiple hypothesis tests. False Discovery Rate (FDR) accomplishes this task by allowing one to control beforehand, the average fraction of false rejections made out of the total number of rejections performed. Furthermore, the FDR procedure is a simple procedure that can be adapted to work with correlated data sets. (from http://www.unt.edu/benchmarks/archives/2002/april02/rss.htm)

AFNI Startup Manual

aclark — 2005-08-27 01:32:18

AFNI Startup Manual

3dfim+

aclark — 2005-08-24 17:54:08

Program to calculate the cross-correlation of an ideal reference waveform with the measured FMRI time series for each voxel.

MTest2

aclark — 2005-08-17 23:51:20

Another Java sample, this one with a rotating rendered brain volume (about 700 KB).

MTest

aclark — 2005-08-17 23:30:12

A Java page for scrolling through brain slices quickly (about 1 MB).

When will you port AFNI to Windows?

rwcox — 2005-08-15 10:30:39

When will you port AFNI to Windows?

afni_build

aclark — 2005-08-15 10:27:47

How to Build AFNI/SUMA on your system (may be outdated)

What does the word AFNI mean?

rwcox — 2005-08-15 10:25:35

What does the word AFNI mean?

Can I use AFNI on a 24-bit X server?

rwcox — 2005-08-15 10:17:33

Can I use AFNI on a 24-bit X server?

What do I do if AFNI crashes?

rwcox — 2005-08-15 10:14:02

What do I do if AFNI crashes?

FMRI

aclark — 2005-08-14 11:34:36

Functional MRI - A technique that helps to pinpoint functional areas of the brain. While the MRI is scanning, the patient is asked to perform a series of activities and movements, such as reading a list or tapping fingers. The areas of the brain that correlate to these movements and activities "light up" on the scan and create an image. This information is used by surgical navigation computers in the planning of incisions, skull openings and tumor removal to minimize neurological deficits.

Command Not Found

aclark — 2005-08-14 11:30:59

You type 'afni' in your terminal and you get 'command not found'. ie. [aclark@elrond ~]$ afni afni: Command not found.

User Written Extensions to AFNI (Plugins)

aclark — 2005-08-11 02:09:30

User Written Extensions to AFNI (Plugins)

How to Program Realtime AFNI

aclark — 2005-08-11 02:05:39

How to Program Realtime AFNI

PostScript notes on registration in FMRI

aclark — 2005-08-11 02:00:40

PostScript notes on registration in FMRI (somewhat old now - based on my presentation at HBM'96 in Boston).

The AFNI TTatlas+tlrc Dataset

aclark — 2005-08-11 01:41:28

The AFNI TTatlas+tlrc Dataset

Creating Regions of Interest (ROI) in AFNI

aclark — 2005-08-11 01:38:52

Creating Regions of Interest (ROI) in AFNI

3dDeconvolve -xjpeg Sample Image

aclark — 2005-08-11 01:31:36

8 runs X polort=1 gives 16 columns of baseline, followed by 8 columns of signal model regressors; there are 1424 time points (vertical axis)

Mike Beauchamp's AFNI Plugin Page

aclark — 2005-08-11 01:19:55

Mike Beauchamp's AFNI Plugin Page

Notes on Parallelizing AFNI Programs

aclark — 2005-08-11 01:12:23

Notes on Parallelizing AFNI Programs

How to Render a Slanted Slab?

rwcox — 2005-08-11 01:08:52

SUMA Usage

aclark — 2005-08-11 00:48:00

SUMA Usage

SUMA Installation

aclark — 2005-08-11 00:47:59

SUMA Installation

Thoughts on Computational Toolsets for Neuroimaging

aclark — 2005-08-11 00:46:30

Thoughts on Computational Toolsets for Neuroimaging

AFNI Colorscales

aclark — 2005-08-11 00:34:01

AFNI Colorscales

FMRI Analysis - NIH Presentation - 31 Mar 2004

aclark — 2005-08-11 00:25:52

PowerPoint presentation given by RW Cox on 31 Mar 2004, outlining FMRI data analysis methods in a nontechnical way. You also need to download the animated GIF files that go with it.

Mapping Data to the Talairach Atlas

aclark — 2005-08-11 00:13:07

A sample script on how to map some numbers to brain regions, using the Talairach-Tournoux Atlas database. For example, put the value 0.379 in each hippocampus voxel, and the value 0.666 in each superior temporal gyrus voxel.

Surface Mapping with AFNI

aclark — 2005-08-10 20:55:10

Surface Mapping with AFNI

Group Analysis Overview

aclark — 2005-08-10 20:55:10

Group Analysis Overview

AFNI Website

aclark — 2005-08-10 20:55:09

AFNI Website

Miscellaneous AFNI Utilities

aclark — 2005-08-10 20:55:08

Miscellaneous AFNI Utilities

Region of Interest (ROI) Drawing

aclark — 2005-08-10 20:55:07

Region of Interest (ROI) Drawing

Volume Rendering

aclark — 2005-08-10 20:55:07

Volume Rendering

Image Input to AFNI - to3d and other data formats

aclark — 2005-08-10 20:55:05

Image Input to AFNI - to3d and other data formats

Introduction and Overview of AFNI

aclark — 2005-08-10 20:55:05

Introduction and Overview of AFNI

HowTo 05 : Analysis of Variance with AFNI '3dANOVA' programs

aclark — 2005-08-10 20:35:10

Analysis of Variance with AFNI '3dANOVA' programs

HowTo 03 : Stimulus Timing Design (intro to AFNI 'RSFgen')

aclark — 2005-08-10 20:35:09

Stimulus Timing Design (intro to AFNI 'RSFgen')

HowTo 02 : Regression Analysis with AFNI '3dDeconvolve'

aclark — 2005-08-10 20:35:08

Regression Analysis with AFNI '3dDeconvolve'

HowTo 01 : Processing Block Design Data with AFNI

aclark — 2005-08-10 20:35:08

Processing Block Design Data with AFNI

waver

aclark — 2005-08-10 20:29:26

to3d

aclark — 2005-08-10 20:29:25

tfim

aclark — 2005-08-10 20:29:25

sqwave

aclark — 2005-08-10 20:29:21

sfim

aclark — 2005-08-10 20:29:20

p2t

aclark — 2005-08-10 20:29:20

nsize

aclark — 2005-08-10 20:29:19

mritopgm

aclark — 2005-08-10 20:29:19

imupsam

aclark — 2005-08-10 20:29:18

imstat

aclark — 2005-08-10 20:29:18

imstack

aclark — 2005-08-10 20:29:18

imrotate

aclark — 2005-08-10 20:29:18

imreg

aclark — 2005-08-10 20:29:17

immask: Apply mask to input 2D image

aclark — 2005-08-10 20:29:17

imdump: Prints out non-zero pixels in a 2D image

aclark — 2005-08-10 20:29:16

Prints out non-zero pixels in a 2D image

imcalc: Do arithmetic on 2D images, voxel-by-voxel

aclark — 2005-08-10 20:29:16

Do arithmetic on 2D images, voxel-by-voxel

imaver: Compute mean and std. dev. of sequence of 2D images

aclark — 2005-08-10 20:29:16

Compute mean and std. dev. of sequence of 2D images

imand: Produce logical "and" of a sequence of input images

aclark — 2005-08-10 20:29:15

Produce logical "and" of a sequence of input images

ftosh: Convert float 2D images to short 2D images

aclark — 2005-08-10 20:29:15

Convert float 2D images to short 2D images

from3d: Extract 2D data files from 3D datasets

aclark — 2005-08-10 20:29:15

Extract 2D data files from 3D datasets

float_scan: Scan input file of floating point numbers for illegal values

aclark — 2005-08-10 20:29:14

Scan input file of floating point numbers for illegal values

fim2: Cross correlation analysis of FMRI 2D time series data

aclark — 2005-08-10 20:29:14

Cross correlation analysis of FMRI 2D time series data

count: Generates strings of numbers

aclark — 2005-08-10 20:29:14

Generates strings of numbers

cdf: Calculates various cumulative distribution probabilities

aclark — 2005-08-10 20:29:13

Calculates various cumulative distribution probabilities

ccalc: Perform interactive arithmetic calculations

aclark — 2005-08-10 20:29:13

Perform interactive arithmetic calculations

byteorder: Indicates host CPU byte order

aclark — 2005-08-10 20:29:12

Indicates host CPU byte order

buckets

aclark — 2005-08-10 20:29:12

adwarp: Resample dataset to grid defined by 'anat parent' dataset

aclark — 2005-08-10 20:29:12

Resample dataset to grid defined by 'anat parent' dataset

abut: Put noncontiguous FMRI slices together (for to3d)

aclark — 2005-08-10 20:29:10

Put noncontiguous FMRI slices together (for to3d)

Table

aclark — 2005-08-10 20:29:09

RSFgen: Generate random stimulus functions

aclark — 2005-08-10 20:29:09

Generate random stimulus functions

Nonparametric

aclark — 2005-08-10 20:29:09

FD2: Visualization of FMRI 2D datasets

aclark — 2005-08-10 20:29:08

Visualization of FMRI 2D datasets

AlphaSim_fig

aclark — 2005-08-10 20:29:08

AlphaSim: Estimate statistical significance via Monte Carlo simulation

aclark — 2005-08-10 20:29:07

Estimate statistical significance via Monte Carlo simulation

4swap: Swap byte quadruples on the files listed

aclark — 2005-08-10 20:29:07

Swap byte quadruples on the files listed

3dvolreg: Register each input 3D sub-brick to a base brick

aclark — 2005-08-10 20:29:07

3dttest: Perform t-test for sets of FMRI 3D datasets

aclark — 2005-08-10 20:29:06

Perform t-test for sets of FMRI 3D datasets

3drotate: Rotate and/or translate all bricks from a 3D dataset

aclark — 2005-08-10 20:29:06

Rotate and/or translate all bricks from a 3D dataset

3drefit: Change information in a 3D dataset's header

aclark — 2005-08-10 20:29:05

Change information in a 3D dataset's header

3dproject: Projection along cardinal axes from a 3D dataset

aclark — 2005-08-10 20:29:05

Projection along cardinal axes from a 3D dataset

3dnvals: Print out the number of sub-bricks in a 3D dataset

aclark — 2005-08-10 20:29:04

Print out the number of sub-bricks in a 3D dataset

3dnoise: Set voxels below noise threshold to zero

aclark — 2005-08-10 20:29:04

Set voxels below noise threshold to zero

3dnewid: Assign a new ID code to a dataset

aclark — 2005-08-10 20:29:03

Assign a new ID code to a dataset

3dmerge: Edit, cluster, filter, and merge FMRI 3D datasets

aclark — 2005-08-10 20:29:03

Edit, cluster, filter, and merge FMRI 3D datasets

3dmaskave: Compute average of all voxels specified by a 3D mask

aclark — 2005-08-10 20:29:02

Compute average of all voxels specified by a 3D mask

3dinfo: Print out useful information from a 3D dataset header file

aclark — 2005-08-10 20:29:02

Print out useful information from a 3D dataset header file

3dhistog

aclark — 2005-08-10 20:29:02

3dfractionize: Resample a mask dataset from a fine grid to a coarse grid

aclark — 2005-08-10 20:29:01

Resample a mask dataset from a fine grid to a coarse grid

3dfim: Cross correlation analysis of FMRI 3D time series data

aclark — 2005-08-10 20:29:01

Cross correlation analysis of FMRI 3D time series data

3ddup: Make duplicate copy of a 3D dataset

aclark — 2005-08-10 20:29:00

Make duplicate copy of a 3D dataset

3dcolon

aclark — 2005-08-10 20:29:00

3dclust: Cluster detection and statistical summary

aclark — 2005-08-10 20:29:00

Cluster detection and statistical summary

3dcalc: Do arithmetic on 3D datasets, voxel-by-voxel

aclark — 2005-08-10 20:28:59

Do arithmetic on 3D datasets, voxel-by-voxel

3dbucket: Concatenate individual sub-bricks into bucket dataset

aclark — 2005-08-10 20:28:59

Concatenate individual sub-bricks into bucket dataset

3dbuc2fim: Convert bucket sub-bricks to fim (fico, etc.) datasets

aclark — 2005-08-10 20:28:58

Convert bucket sub-bricks to fim (fico, etc.) datasets

3daxialize

aclark — 2005-08-10 20:28:58

3dWilcoxon

aclark — 2005-08-10 20:28:57

3dWavelets

aclark — 2005-08-10 20:28:57

3dTsmooth: Smooth each voxel time series in a 3D+time dataset

aclark — 2005-08-10 20:28:57

Smooth each voxel time series in a 3D+time dataset

3dTcat: Concatenate sub-bricks into one 3D+time dataset

aclark — 2005-08-10 20:28:56

Concatenate sub-bricks into one 3D+time dataset

3dTSgen: Generates random signal+noice 3D datasets

aclark — 2005-08-10 20:28:56

Generates random signal+noice 3D datasets

3dStatClust

aclark — 2005-08-10 20:28:55

3dNLfim Nonlinear Regression Analysis of FMRI time series data

aclark — 2005-08-10 20:28:54

Nonlinear Regression Analysis of FMRI time series data

3dMannWhitney: Nonparametric Mann-Whitney rank-sum two sample test

aclark — 2005-08-10 20:28:53

Nonparametric Mann-Whitney rank-sum two sample test

3dKruskalWallis: Nonparametric Kruskal-Wallis test for multiple samples

aclark — 2005-08-10 20:28:53

Nonparametric Kruskal-Wallis test for multiple samples

3dIntracranial: Automatic segmentation of intracranial region

aclark — 2005-08-10 20:28:52

Automatic segmentation of intracranial region

3dFriedman: Nonparametric Friedman test for blocked multiple sample

aclark — 2005-08-10 20:28:52

Nonparametric Friedman test for blocked multiple sample

3dFWHM: Estimation of image Filter Width Half Maximum

aclark — 2005-08-10 20:28:52

Estimation of image Filter Width Half Maximum

3dFDR

aclark — 2005-08-10 20:28:51

3dExtrema

aclark — 2005-08-10 20:28:51

3T_toafni: Send information about imaging sequence to AFNI

aclark — 2005-08-10 20:28:46

Send information about imaging sequence to AFNI

2swap: Swap byte pairs for inter-operating system compatibility

aclark — 2005-08-10 20:28:46

Swap byte pairs for inter-operating system compatibility

2dImReg: Slice-by-slice image registration of FMRI 3D datasets

aclark — 2005-08-10 20:28:45

Slice-by-slice image registration of FMRIF 3D datasets

24swap: Swaps byte pairs and/or quadruples on listed files

aclark — 2005-08-10 20:28:45

Swaps byte pairs and/or quadruples on listed files

1dplot: Graph columns of *.1D type time series to screen

aclark — 2005-08-10 20:28:44

Graph columns of *.1D type time series to screen

3dvolreg

aclark — 2005-08-10 15:38:31

3dttest

aclark — 2005-08-10 15:38:30

3drotate

aclark — 2005-08-10 15:38:30

3dretroicor

aclark — 2005-08-10 15:38:29

3dresample

aclark — 2005-08-10 15:38:29

3drename

aclark — 2005-08-10 15:38:29

3drefit

aclark — 2005-08-10 15:38:28

3dproject

aclark — 2005-08-10 15:38:28

3dpc

aclark — 2005-08-10 15:38:27

3dnvals

aclark — 2005-08-10 15:38:27

3dnoise: Usage: 3dnoise [-blast] [-snr fac] [-nl x ] datasets ...

aclark — 2005-08-10 15:38:26

3dnewid

aclark — 2005-08-10 15:38:25

3dmerge

aclark — 2005-08-10 15:38:25

3dmaskdump

aclark — 2005-08-10 15:38:24

3dmaskave

aclark — 2005-08-10 15:38:24

3dinfo: Usage: 3dinfo [-verb OR -short] dataset [dataset ...]

aclark — 2005-08-10 15:38:23

3dhistog: Usage: 3dhistog [editing options] [histogram options] dataset

aclark — 2005-08-10 15:38:23

3dfractionize

aclark — 2005-08-10 15:38:22

3dfimplus

aclark — 2005-08-10 15:38:22

3dfim: Usage: 3dfim [-im1 num] -input fname -prefix name

aclark — 2005-08-10 15:38:21

3ddup: Usage: 3ddup [options] dataset

aclark — 2005-08-10 15:38:20

3ddot: Usage: 3ddot [options] dset1 dset2

aclark — 2005-08-10 15:38:20

3ddelay

aclark — 2005-08-10 15:38:19

3dcopy: Usage 1: 3dcopy [-verb] [-denote] old_prefix new_prefix

aclark — 2005-08-10 15:38:18

3dclust: Usage: 3dclust [editing options] [other options] rmm vmul dset ...

aclark — 2005-08-10 15:38:17

3dcalc

aclark — 2005-08-10 15:38:17

3dbucket

aclark — 2005-08-10 15:38:17

3dbuc2fim: Usage: 3dbucket options

aclark — 2005-08-10 15:38:16

3daxialize: Usage: 3daxialize [options] dataset

aclark — 2005-08-10 15:38:16

3dZregrid: Usage: 3dZregrid [option] dataset

aclark — 2005-08-10 15:38:15

3dZeropad: Usage: 3dZeropad [options] dataset

aclark — 2005-08-10 15:38:15

3dZcutup: Usage: 3dZcutup [options] dataset

aclark — 2005-08-10 15:38:15

3dZcat: Usage: 3dZcat [options] dataset dataset ...

aclark — 2005-08-10 15:38:14

3dWinsor: Usage: 3dWinsor [options] dataset

aclark — 2005-08-10 15:38:14

3dWilcoxon

aclark — 2005-08-10 15:38:13

3dWavelets

aclark — 2005-08-10 15:38:13

3dWarpDrive: Usage: 3dWarpDrive [options] dataset

aclark — 2005-08-10 15:38:12

3dWarp: Usage: 3dWarp [options] dataset

aclark — 2005-08-10 15:38:11

3dVol2Surf: usage: 3dVol2Surf [options] -spec SPEC_FILE -sv SURF_VOL

aclark — 2005-08-10 15:38:10

3dUniformize

aclark — 2005-08-10 15:38:10

3dUndump: Usage: 3dUndump [options] infile ...

aclark — 2005-08-10 15:38:09

3dTstat: Usage: 3dTstat [options] dataset

aclark — 2005-08-10 15:38:09

3dTsmooth: Usage: 3dTsmooth [options] dataset

aclark — 2005-08-10 15:38:08

3dTshift: Usage: 3dTshift [options] dataset

aclark — 2005-08-10 15:38:08

3dTqual: Usage: 3dTqual [options] dataset

aclark — 2005-08-10 15:38:07

3dToutcount: Usage: 3dToutcount [options] dataset

aclark — 2005-08-10 15:38:07

3dThreetoRGB: Usage #1: 3dThreetoRGB [options] dataset

aclark — 2005-08-10 15:38:06

3dTcorrelate: Usage: 3dTcorrelate [options] xset yset

aclark — 2005-08-10 15:38:06

3dTcat

aclark — 2005-08-10 15:38:06

3dTagalign: Usage: 3dTagalign [options] dset

aclark — 2005-08-10 15:38:05

3dTSgen

aclark — 2005-08-10 15:38:05

3dSurfMaskDump

aclark — 2005-08-10 15:38:05

3dSurfMask: Usage: 3dSurfMask <-i_TYPE SURFACE> <-prefix PREFIX>

aclark — 2005-08-10 15:38:04

3dSurf2Vol: usage: 3dSurf2Vol [options] -spec SPEC_FILE -surf_A SURF_NAME

aclark — 2005-08-10 15:38:04

3dStatClust: Usage: 3dStatClust options datasets

aclark — 2005-08-10 15:38:03

3dSpatNorm: Usage: 3dSpatNorm [options] dataset

aclark — 2005-08-10 15:38:03

3dSkullStrip

aclark — 2005-08-10 15:38:03

3dRowFillin: Usage: 3dRowFillin [options] dataset

aclark — 2005-08-10 15:38:02

3dRegAna

aclark — 2005-08-10 15:38:02

3dROIstats: Usage: 3dROIstats -mask[n] mset [options] datasets

aclark — 2005-08-10 15:38:02

3dOverlap: Usage: 3dOverlap [options] dset1 dset2 ...

aclark — 2005-08-10 15:38:01

3dNotes: Usage: 3dNotes [-a "string"] [-h "string"][-d num] [-help] dataset

aclark — 2005-08-10 15:38:01

3dNLfim

aclark — 2005-08-10 15:38:00

3dMedianFilter: Usage: 3dMedianFilter [options] dataset

aclark — 2005-08-10 15:38:00

3dMean: Usage: 3dMean [options] dset dset ...

aclark — 2005-08-10 15:37:59

3dMax: Usage: 3dMax [options] dataset

aclark — 2005-08-10 15:37:59

3dMannWhitney

aclark — 2005-08-10 15:37:59

3dMINCtoAFNI: Usage: 3dMINCtoAFNI [-prefix ppp] dataset.mnc

aclark — 2005-08-10 15:37:58

3dLRflip: Usage: 3dLRflip [-prefix ppp] dataset

aclark — 2005-08-10 15:37:58

3dKruskalWallis

aclark — 2005-08-10 15:37:57

3dIntracranial

aclark — 2005-08-10 15:37:57

3dFriedman

aclark — 2005-08-10 15:37:57

3dFourier: Usage: 3dFourier [options] dataset

aclark — 2005-08-10 15:37:57

3dExtrema: Usage: 3dExtrema options datasets

aclark — 2005-08-10 15:37:56

3dEntropy: Usage: 3dEntropy dataset ...

aclark — 2005-08-10 15:37:56

3dDetrend: Usage: 3dDetrend [options] dataset

aclark — 2005-08-10 15:37:55

3dDespike: Usage: 3dDespike [options] dataset

aclark — 2005-08-10 15:37:55

3dDeconvolve_f

aclark — 2005-08-10 15:37:55

3dDeconvolve

aclark — 2005-08-10 15:37:54

3dDWItoDT: Usage: 3dDWItoDT [options] gradient-file dataset

aclark — 2005-08-10 15:37:54

3dDTeig: Usage: 3dDTeig [options] dataset

aclark — 2005-08-10 15:37:54

3dConvolve

aclark — 2005-08-10 15:37:54

3dClipLevel: Usage: 3dClipLevel [options] dataset

aclark — 2005-08-10 15:37:54

3dCRUISEtoAFNI: Usage: 3dCRUISEtoAFNI -input CRUISE_HEADER.dx

aclark — 2005-08-10 15:37:53

3dCM: Usage: 3dCM [options] dset

aclark — 2005-08-10 15:37:53

3dBRAIN_VOYAGERtoAFNI: Usage: 3dBRAIN_VOYAGERtoAFNI -input BV_VOLUME.vmr

aclark — 2005-08-10 15:37:53

3dAutomask: Usage: 3dAutomask [options] dataset

aclark — 2005-08-10 15:37:53

3dAutobox: Usage: 3dAutobox dataset

aclark — 2005-08-10 15:37:53

3dAutoTcorrelate: Usage: 3dAutoTcorrelate [options] dset

aclark — 2005-08-10 15:37:52

3dAttribute: Usage: 3dAttribute [options] aname dset

aclark — 2005-08-10 15:37:52

3dAnhist: Usage: 3dAnhist [options] dataset

aclark — 2005-08-10 15:37:52

3dAnatNudge: Usage: 3dAnatNudge [options]

aclark — 2005-08-10 15:37:52

3dANOVA3

aclark — 2005-08-10 15:37:52

3dANOVA2

aclark — 2005-08-10 15:37:51

3dANOVA

aclark — 2005-08-10 15:37:51

3dANALYZEtoAFNI: Usage: 3dANALYZEtoAFNI [options] file1.hdr file2.hdr ...

aclark — 2005-08-10 15:37:51

3dAFNItoNIML: Usage: 3dAFNItoNIML [options] dset

aclark — 2005-08-10 15:37:51

3dAFNItoNIFTI: Usage: 3dAFNItoNIFTI [options] dataset

aclark — 2005-08-10 15:37:50

3dAFNItoMINC: Usage: 3dAFNItoMINC [options] dataset

aclark — 2005-08-10 15:37:50

3dAFNItoANALYZE: Usage: 3dAFNItoANALYZE [-4D] [-orient code] aname dset

aclark — 2005-08-10 15:37:50

3dAFNIto3D: Usage: 3dAFNIto3D [options] dataset

aclark — 2005-08-10 15:37:49

1dplot: Usage: 1dplot [options] tsfile ...

aclark — 2005-08-10 15:00:33

1dnorm: Usage: 1dnorm infile outfile

aclark — 2005-08-10 15:00:33

1dgrayplot: Usage: 1dgrayplot [options] tsfile

aclark — 2005-08-10 15:00:32

1dfft: Usage: 1dfft [options] infile outfile

aclark — 2005-08-10 15:00:31

1deval: Usage: 1deval [options] -expr 'expression'

aclark — 2005-08-10 15:00:31

2swap

aclark — 2005-08-10 14:59:16

2dImReg

aclark — 2005-08-10 14:59:16

24swap: Usage: 24swap [options] file ...

aclark — 2005-08-10 14:59:15

whirlgif

aclark — 2005-08-10 14:45:22

whereami

aclark — 2005-08-10 14:45:22

waver

aclark — 2005-08-10 14:45:22

to3d

aclark — 2005-08-10 14:45:21

tfim

aclark — 2005-08-10 14:45:21

suma_change_spec

aclark — 2005-08-10 14:45:20

suma

aclark — 2005-08-10 14:45:20

strblast

aclark — 2005-08-10 14:45:19

sqwave

aclark — 2005-08-10 14:45:19

siemens_vision

aclark — 2005-08-10 14:45:19

sfim

aclark — 2005-08-10 14:45:18

serial_helper

aclark — 2005-08-10 14:45:18

rtfeedme

aclark — 2005-08-10 14:45:17

rotcom

aclark — 2005-08-10 14:45:17

rmz

aclark — 2005-08-10 14:45:16

quickspec

aclark — 2005-08-10 14:45:16

plugout_tt

aclark — 2005-08-10 14:45:16

plugout_ijk

aclark — 2005-08-10 14:45:15

plugout_drive

aclark — 2005-08-10 14:45:15

p2t

aclark — 2005-08-10 14:45:14

nsize

aclark — 2005-08-10 14:45:14

nifti_tool

aclark — 2005-08-10 14:45:14

nifti_stats

aclark — 2005-08-10 14:45:13

nifti1_test

aclark — 2005-08-10 14:45:13

mritopgm

aclark — 2005-08-10 14:45:12

mpegtoppm

aclark — 2005-08-10 14:45:12

mpeg_encode

aclark — 2005-08-10 14:45:12

mayo_analyze

aclark — 2005-08-10 14:45:11

make_stim_file

aclark — 2005-08-10 14:45:11

inspec

aclark — 2005-08-10 14:45:11

imupsam

aclark — 2005-08-10 14:45:09

imstat

aclark — 2005-08-10 14:45:09

imstack

aclark — 2005-08-10 14:45:08

imrotate

aclark — 2005-08-10 14:45:08

imreg

aclark — 2005-08-10 14:45:07

immask

aclark — 2005-08-10 14:45:07

imdump

aclark — 2005-08-10 14:45:07

imcutup

aclark — 2005-08-10 14:45:06

imcalc

aclark — 2005-08-10 14:45:06

imaver

aclark — 2005-08-10 14:45:05

imand

aclark — 2005-08-10 14:45:05

ge_header

aclark — 2005-08-10 14:45:05

ftosh

aclark — 2005-08-10 14:45:04

from3d

aclark — 2005-08-10 14:45:04

float_scan

aclark — 2005-08-10 14:45:03

fim2

aclark — 2005-08-10 14:45:03

file_tool

aclark — 2005-08-10 14:45:02

fftest

aclark — 2005-08-10 14:45:02

ent16

aclark — 2005-08-10 14:45:01

djpeg

aclark — 2005-08-10 14:45:01

dicom_to_raw

aclark — 2005-08-10 14:45:00

dicom_hdr

aclark — 2005-08-10 14:45:00

count

aclark — 2005-08-10 14:44:59

cjpeg

aclark — 2005-08-10 14:44:59

cdf

aclark — 2005-08-10 14:44:59

ccalc

aclark — 2005-08-10 14:44:58

cat_matvec

aclark — 2005-08-10 14:44:58

byteorder

aclark — 2005-08-10 14:44:58

aiv

aclark — 2005-08-10 14:44:57

adwarp

aclark — 2005-08-10 14:44:52

abut

aclark — 2005-08-10 14:44:51

Xphace

aclark — 2005-08-10 14:44:51

Vecwarp

aclark — 2005-08-10 14:44:50

UpdateAfni

aclark — 2005-08-10 14:44:50

SurfaceMetrics

aclark — 2005-08-10 14:44:49

SurfToSurf

aclark — 2005-08-10 14:44:49

SurfSmooth

aclark — 2005-08-10 14:44:48

SurfQual

aclark — 2005-08-10 14:44:48

SurfPatch

aclark — 2005-08-10 14:44:48

SurfMesh

aclark — 2005-08-10 14:44:47

SurfMeasures

aclark — 2005-08-10 14:44:47

SurfClust

aclark — 2005-08-10 14:44:46

ScaleToMap

aclark — 2005-08-10 14:44:46

SampBias

aclark — 2005-08-10 14:44:46

SUMA_Make_Spec_SF

aclark — 2005-08-10 14:44:45

SUMA_Make_Spec_FS

aclark — 2005-08-10 14:44:45

SUMA_AlignToExperiment

aclark — 2005-08-10 14:44:44

RenamePanga

aclark — 2005-08-10 14:44:44

aclark — 2005-08-10 14:44:43

ROI2dataset

aclark — 2005-08-10 14:44:43

NoExt

aclark — 2005-08-10 14:44:43

MapIcosahedron

aclark — 2005-08-10 14:44:42

MakeColorMap

aclark — 2005-08-10 14:44:41

IsoSurface

aclark — 2005-08-10 14:44:41

Imon

aclark — 2005-08-10 14:44:40

Ifile

aclark — 2005-08-10 14:44:39

GetAfniView

aclark — 2005-08-10 14:44:39

GetAfniPrefix

aclark — 2005-08-10 14:44:38

FSread_annot

aclark — 2005-08-10 14:44:37

FD2

aclark — 2005-08-10 14:44:36

CreateIcosahedron

aclark — 2005-08-10 14:44:36

ConvexHull

aclark — 2005-08-10 14:44:35

ConvertSurface

aclark — 2005-08-10 14:44:35

ConvertDset

aclark — 2005-08-10 14:44:34

CompareSurfaces

aclark — 2005-08-10 14:44:34

CommandGlobb

aclark — 2005-08-10 14:44:34

AlphaSim

aclark — 2005-08-10 14:44:33

Align_Centers

aclark — 2005-08-10 14:44:33

4swap

aclark — 2005-08-10 14:44:32

4Daverage

aclark — 2005-08-10 14:44:31

1dsvd

aclark — 2005-08-09 21:52:49

afni_vcheck

aclark — 2005-08-09 21:07:42

The plugins are written for AFNI98.

aclark — 2005-08-09 20:52:38

The plugins are written for AFNI98.

Reading Datasets Across the Web

aclark — 2005-08-09 20:52:38

Reading Datasets Across the Web

Using 3dvolreg and 3drotate to Align Intra-Subject Inter-Session Datasets

aclark — 2005-08-09 20:52:38

Using 3dvolreg and 3drotate to Align Intra-Subject Inter-Session Datasets

Setting Up AFNI Colors and Palettes

aclark — 2005-08-09 20:52:37

Setting Up AFNI Colors and Palettes

Region-of-Interests (ROIs) in AFNI

aclark — 2005-08-09 20:52:37

Region-of-Interests (ROIs) in AFNI

Format of AFNI Rendering Scripts

aclark — 2005-08-09 20:52:36

Format of AFNI Rendering Scripts

Notes on Image and Volume Registration in AFNI 2.21+

aclark — 2005-08-09 20:52:36

Notes on Image and Volume Registration in AFNI 2.21+

Realtime AFNI control information: What it needs

aclark — 2005-08-09 20:52:35

Realtime AFNI control information: What it needs

Plugout Instructions

aclark — 2005-08-09 20:52:35

Plugout Instructions

The following is the README file for the permutation test plugins written by Matthew Belmonte. This code has been released under the GPL.

aclark — 2005-08-09 20:52:34

The following is the README file for the permutation test plugins written by Matthew Belmonte. This code has been released under the GPL.

Programming Information for Notes and History

aclark — 2005-08-09 20:52:34

Programming Information for Notes and History

Anatomical Dataset Types

aclark — 2005-08-09 20:52:33

Anatomical Dataset Types

Unix Environment Variables Used by AFNI

aclark — 2005-08-09 20:52:33

Unix Environment Variables Used by AFNI

Driving AFNI from a Plugout or a Startup Script

aclark — 2005-08-09 20:52:32

Driving AFNI from a Plugout or a Startup Script

aclark — 2005-08-09 20:52:32

Compressed Dataset .BRIK Files

aclark — 2005-08-09 20:52:31

Compressed Dataset .BRIK Files

Video Demo: Grayscale Adjustment

aclark — 2005-08-09 20:00:13

Adjusting the image grayscale with mouse gestures. [Quicktime: 6.4 MB]

Video Demo: Image and Graph Viewers

aclark — 2005-08-09 19:48:50

Animating through space and time in the AFNI Image and Graph viewers. [Quicktime: 11.3 MB]

Video Demo: Threshold and Pbar Locking - MPEG

aclark — 2005-08-09 19:40:48

Same as above [MPEG: 20 MB]

Video Demo: Threshold and Pbar Locking

aclark — 2005-08-09 19:35:38

Demonstration of threshold slider and color pbar locking, now with a sound track! [Quicktime: 3.8 MB; 2:03]

Video Demo: Image Projection

aclark — 2005-08-09 18:06:22

Video Demonstration: Minimum Intensity Projection with the AFNI Image Controller (Dataset is 512x512 MR Venogram) [QuickTime: 1.5 MB; 0:26]

afni_download

aclark — 2005-08-09 16:22:01

AFNI/SUMA Download Techniques

Cygwin Build Instructions

rwcox — 2005-08-09 15:53:33

Cygwin Build Instructions

Mac OS X Build Instructions

aclark — 2005-08-09 15:37:41

Mac OS X Build Instructions

What are your pet peeves about FMRI?

rwcox — 2005-08-01 14:53:33

Can I send you some data?

rwcox — 2005-08-01 14:53:33

What is the format of the TTatlas+tlrc dataset?

rwcox — 2005-08-01 14:53:32

How can I remove a subject's name from an image file?

rwcox — 2005-08-01 14:53:31

How can I take a mask from +tlrc/+acpc back to +orig?

rwcox — 2005-08-01 14:53:30

After 3dZeropad-ing, where are the Talairach markers?

rwcox — 2005-08-01 14:53:30

How can I extract a voxel timeseries to a text file?

rwcox — 2005-08-01 14:53:29

How can I normalize the sub-bricks in a 3D+time dataset?

rwcox — 2005-08-01 14:53:28

what is Resampling?

rwcox — 2005-08-01 14:53:27

Can I use AFNI or its code at my company?

rwcox — 2005-08-01 14:53:26

How can I edit the History Note in a dataset?

rwcox — 2005-08-01 14:53:24

I'm losing data when I use the "Nudge" plugin on functional datasets!?

rwcox — 2005-08-01 14:34:58

How can I do SPM-like analyses with AFNI?

rwcox — 2005-08-01 14:34:58

How can I compare 'small' and 'big' Talairach box datasets?

rwcox — 2005-08-01 14:34:57

How can I figure out the format an image file is in?

rwcox — 2005-08-01 14:34:56

How can I use scripts to change datasets in the volume rendering plugin?

rwcox — 2005-08-01 14:34:55

What is "Warp on Demand"?

rwcox — 2005-08-01 14:34:55

How can I read ASCII image files into to3d?

rwcox — 2005-08-01 14:34:54

How can I add my own function to the FIM+ menu?

rwcox — 2005-08-01 14:34:53

How can I mask off "function" outside the brain?

rwcox — 2005-08-01 14:34:52

How many sites use AFNI?

rwcox — 2005-08-01 14:18:40

Are the Talairach coordinates from AFNI the same as from SPM?

rwcox — 2005-08-01 14:18:39

What good is the "Anatomy Parent" in to3d?

rwcox — 2005-08-01 14:18:37

How can I get an image from AFNI into a paint/drawing program?

rwcox — 2005-08-01 14:18:36

Why are my 3D+time datasets so huge when I resample them to Talairach coordinates?

rwcox — 2005-08-01 14:18:35

How does the Range setting interact with the color pbar scale?

rwcox — 2005-08-01 14:18:34

Do you offer a course on using the AFNI package?

rwcox — 2005-08-01 14:18:34

What are some known problems with the AFNI package?

rwcox — 2005-08-01 14:18:33

How can I do a t-test on time series data?

rwcox — 2005-08-01 14:18:32

After 3dmerge, I don't have any threshold data?

rwcox — 2005-08-01 14:18:31

Is there a faster way to average datasets than using 3dcalc?

rwcox — 2005-07-31 23:38:38

How can I suppress the spuriously large % Change values from FIM+?

rwcox — 2005-07-31 23:38:37

How can I turn off the "Splash" window that AFNI starts with?

rwcox — 2005-07-31 23:38:37

How can I use the volume renderer to deal with arbitrary datasets?

rwcox — 2005-07-31 23:38:36

Can you supply me with the images from the Talairach-Tournoux Atlas?

rwcox — 2005-07-31 23:38:35

If i change a timeseries file, why doesn't Rescan *.1D re-read it?

rwcox — 2005-07-31 23:38:35

When trying to compile AFNI, I get messages like "Xm/Xmall.h not found"!

rwcox — 2005-07-31 23:38:34

I installed the AFNI package, but when I try to run a program, I get a 'not found' message!

rwcox — 2005-07-31 23:38:34

I duplicated a plugin and then edited it, but can't get both it and the original to work at once!

rwcox — 2005-07-31 23:38:33

What are the FIM+ sub-bricks?

rwcox — 2005-07-31 23:38:32

What is the format of a .HEAD file?

rwcox — 2005-07-31 23:14:26

What is the format of a .BRIK file?

rwcox — 2005-07-31 23:13:10

How can I "upsample" an image to higher resolution?

rwcox — 2005-07-31 23:13:09

How can I more easily control the initial colors in the functional overlays?

rwcox — 2005-07-31 23:13:09

How can I count the number of voxels above threshold in a functional dataset?

rwcox — 2005-07-31 23:13:08

What does the "Intensity" computed by FIM mean?

rwcox — 2005-07-31 23:13:08

How can I avoid having AFNI convert the symbolic links in my session directory names?

rwcox — 2005-07-31 23:13:07

How can I avoid running out of memory in to3d?

rwcox — 2005-07-31 23:13:06

What are "Arg list too long" messages?

rwcox — 2005-07-31 23:13:06

What are the angles reported from 3dvolreg?

rwcox — 2005-07-31 23:13:05

How can I do Region-of-Interest (ROI) analyses?

rwcox — 2005-07-31 10:46:40

How would you configure a Linux system for AFNI?

rwcox — 2005-07-31 10:46:39

Can I resample to a non-cubical grid using AFNI?

rwcox — 2005-07-31 10:46:38

What are "-tim:zt" and -time:tz" in to3d?

rwcox — 2005-07-31 10:46:37

How do I make a GIF animation?

rwcox — 2005-07-31 10:46:37

I wrote a plugin that worked, so why does it fail when I download a new version of AFNI?

rwcox — 2005-07-31 10:46:36

So how do the clustering paramerters "rmm" and "vmul" work?

rwcox — 2005-07-31 10:46:35

How do I get a list of Talairach coordinates?

rwcox — 2005-07-31 10:46:35

How do I control the overlay colors?

rwcox — 2005-07-31 10:46:34

The grayscale image display of my dataset doesn't seem right.

rwcox — 2005-07-31 10:46:33

How do I read images from format "X"?

rwcox — 2005-07-31 10:31:00

How can I see the numerical value stored in a voxel?

rwcox — 2005-07-31 10:31:00

Are there any man pages for AFNI programs?

rwcox — 2005-07-31 10:31:00

How do I transport image data to a system with swapped bytes?

rwcox — 2005-07-31 10:31:00

What functions are used in program waver?

rwcox — 2005-07-31 10:30:59

My anatomical and functional data are oblique!?

rwcox — 2005-07-31 10:30:59

I want to input some 8 bit images. How?

rwcox — 2005-07-31 10:30:58

to3d and other programs can't read legal image files. What gives?

rwcox — 2005-07-31 10:30:58

Yes, but what about Mayo ANALYZE, or Matlab?

rwcox — 2005-07-31 10:30:57

How do I choose the color displayed for zero image intensity?

rwcox — 2005-07-31 10:18:35

How do I control the grayscale in an image window?

rwcox — 2005-07-31 10:18:34

How do I hide the controls in an image display window?

general — 2005-07-31 10:18:31

What do I do if I click on the wrong place in an image?

rwcox — 2005-07-31 10:18:29

What do I do if I run out of colors?

rwcox — 2005-07-31 10:18:26

Are there any "fun" features in AFNI?

rwcox — 2005-07-31 10:18:12