Classified program list

All AFNI programs, great and small, are listed here and classified based on functionality. That is, they are grouped into some general categories that we made up and given short bios.

The ranking of each program is to highlight ones that we think are particularly useful in general processing (‘5’ being the most directly useful, and ‘1’ being something that might just be a low-level, supplementary tool). Note that a given program may appear in more than one group.

This page might be most useful by using your browser to search through the text for keywords of interest, such as “ROI”, “mask”, “diffusion”, “align”, “model”, etc. Clicking on the name of the program will bring you its online help documentation, referenced from this page of all AFNI “helps”.


Interactive viewer GUIs

5

afni

GUI-based viewer for exploring data primarily as slices

5

suma

GUI-based viewer for exploring data in 3D: surfaces, tracts, graph nodes, and volume slices

2

aiv

AFNI Image Viewer program

Voxelwise calcs, esp. stats and tests

5

3dttest++

Compute voxelwise t-tests (and GLMs) across collection of datasets (see 3dMEMA for generalizing to include within-subjects variance in model)

5

3dTstat

Compute voxelwise statistics of time series datasets (e.g., mean, variance)

5

3dMVM

Group-analysis program that performs traditional ANOVA- and ANCOVA style computations, and multivariate modeling

5

3dLME

Group-analysis program that performs linear mixed-effects (LME) modeling analysis

5

3dMEMA

Group-analysis program that performs Mixed Effects Meta Analysis, modeling both within- and across-subjects variability

4

3dMean

Compute the average of a number of datasets

3

3dGroupInCorr

With a group of dsets, calc voxelwise t-tests on group of corr maps wherever user clicks

3

3dTcorr1D

Correlation coefficient between 3D+time dataset and 1D time series

3

3dTcorrMap

Compute average correlation of every voxel with every other

1

3dSetupGroupInCorr

Preliminary program to run when using 3dGroupInCorr

1

3dClustSim

3Monte Carlo simulation for multiple comparison correction

1

3dTcorrelate

Compute correlation between two 3D+time datasets

1

3dTfitter

Fit a linear model to each voxel time series, with various methods (L1, L2, LASSO)

1

3dTfilter

Apply a linear filter to each voxel time series (archaic)

1

3dTsort

Sort each voxel’s time series in various ways

1

3dRank

1

3dRankizer

1

3dANOVA

1-way ANOVA (fixed effects)

1

3dANOVA2

2-way ANOVA (fixed, random, mixed effects)

1

3dANOVA3

3-way ANOVA (fixed, random, mixed effects)

1

3dExtractGroupInCorr

1

3dFDR

False Discovery Rate analysis

1

AlphaSim

(obsolete -> use 3dClustSim)

1

1dSEM

Structural equation modeling (path analysis) (why here???)

1

3dWilcoxon

Nonparametric Wilcoxon test

1

3dKruskalWallis

Nonparametric Kruskal-Wallis test

1

3dFriedman

Nonparametric Friedman test

1

3dMannWhitney

Nonparametric 3dMannWhitney test

1

3dRegAna

Voxel-wise linear regression analyses

1

3dttest

(obsolete -> use 3dttest++)

1

3dPval

Convert each statistical value in a dataset (e.g., t-statistic) to a p-value

1

3dNormalityTest

Tests the input values at each voxel for normality, using the Anderson-Darling method

Get info/stats within ROIs

5

whereami

Get atlas region name for coordinates

4

3dROIstats

Calculate dataset values from multiple ROIs

4

3dmaskave

Calculate dataset values averaged over a ROI

4

3dmaskdump

Output all dataset values in a ROI

4

3dBrickStat

Calculate percentile values within dsets

4

@measure_bb_thick

measure thickness using ball and box method

4

@measure_erosion_thick

measure thickness using erosion method

4

@measure_in2out

measure thickness between in and out masks

4

@thickness_master

compare thickness measurement methods

3

3dUndump

Create dataset from text (inverse of 3dmaskdump)

2

3dfractionize

Resample a mask dataset to a different resolution

1

3dMax

(obsolete -> use 3dBrickStat)

1

3dOverlap

Create mask that is overlap of nonzero voxels from multiple datasets

1

3dTto1D

Collapse 4D data to 1D in various ways

1

@Atlasize

Make an atlas from a dataset and label text files

1

@MakeLabelTable

Assign labels to values

1

AFNI_atlas_spaces.niml

space, atlas, transformations definitions file

Build FMRI pipelines

5

afni_proc.py

Generate tcsh script for processing single subject FMRI data

4

gen_ss_review_scripts.py

Generate QC review scripts

3

gen_group_command.py

Generate group analysis scripts

2

uber_subject.py

Graphical interface to help set up an afni_proc.py command (probably just use -> afni_proc.py directly; uber_subject.py does not have full range of options that afni_proc.py has; recommended to use afni_proc.py examples as a basis, instead)

1

uber_proc.py

1

afni_restproc.py

(obsolete -> use afni_proc.py)

Align/register/warp/axialize spatially

5

3dvolreg

Volumetric registration (rigid body in 3D, 6DOF linear)

5

align_epi_anat.py

Align 2 volumes (e.g. anat and EPI)

5

3dQwarp

Align two datasets using nonlinear warping (relatedly, see @SSwarper, auto_warp.py, @toMNI_Qwarpar)

5

3dAllineate

Cross-modality affine volume registration

5

3dresample

Rewrite dataset in new orientation, with new voxel size

4

fat_proc_align_anat_pair

Align a T1w dset to a T2w dset, esp. as part of DWI processing and if incorporating FreeSurfer after

4

fat_proc_axialize_anat

Attempt to align major viewing planes of anatomical with FOV, based on WB alignment to a reference vol

4

3dNwarpApply

Apply a nonlinear warp to transform a dataset

3

@Align_Centers

Align the center of a dataset to another

3

@AddEdge

Show two or more datasets with edges for alignment visualization

1

auto_warp.py

wrapper for nonlinear warping with 3dQwarp

1

@auto_tlrc

Automatic transformation of dataset to match Talairach template (rigid/12dof???)

1

afni_proc.py

Can wrap many registration operations

1

3dWarp

Non-rigid transformation of 3D coordinates

1

3dWarpDrive

Volumetric registration, includes warping (12DOF, linear affine); prob use 3dAllineate or align_epi_anat.py (???)

1

@align_partial_oblique

Align (non-oblique) full- and partial-coverage T1w datasets; consider 3dQwarp instead.

1

@auto_align

(obsolete -> use align_epi_anat.py)

1

@SSwarper

Skull-stripping program that uses a reference anatomical

1

@SUMA_AlignToExperiment

Align volume from FreeSurfer analysis to a different session’s anatomical volume in order to warp surfaces similarly

1

3dNwarpAdjust

Adjust a collection of nonlinear warps for template building (@toMNI_Qwarpar)

1

3dNwarpCalc

Carry out calculations on nonlinear warps

1

3dNwarpCat

Combine linear and nonlinear warps (spatial transformations)

1

3dNwarpFuncs

Compute various voxelwise information about a nonlinear warp (e.g., Jacobian)

1

3dNwarpXYZ

Apply a nonlinear warp to a set of (x,y,z) triples

1

3dTagalign

Align datasets by matching manually placed ‘tags’

1

plugin(Edit Tagset)

Place ‘tags’ in a dataset interactively

1

3drotate

Rigid body rotation of dataset in 3D

1

3dAnatNudge

(obsolete -> use align_epi_anat.py); try to align EPI and structural volumes automatically

1

cat_matvec

Utility for combining linear affine transformation matrices (e.g., from 3dAllineate)

1

adwarp

Transform dataset using warp from dataset header

1

Vecwarp

Transform 3-vectors using warp from dataset header

1

2dImReg

Slice-by-slice registration (rigid body in 2D)

1

3daxialize

(obsolete -> use 3dresample)

1

lpc_align.py

(obsolete -> use align_epi_anat.py)

1

@toMNI_Awarp

Make a group template - affine alignment

1

@toMNI_Qwarpar

Make a group template - iterative nonlinear alignment

1

uber_align_test.py

GUI for affine alignment with align_epi_anat.py

1

unWarpEPI.py

Blip-up/down unwarping nonlinear alignment

1

@Shift_Volume

Move origin of dataset by specified amount or shift between MNI and MNI_ANAT

SUMA surface calculations, formats and viewing

5

@SUMA_Make_Spec_FS

Convert Freesurfer surfaces to SUMA spec files

4

IsoSurface

Extract isosurface from a volume

4

3dSurf2Vol

Compute volume equivalent from surface or pair of surfaces

4

3dVol2Surf

Assign values to surface nodes from volumetric data

4

DriveSuma

Send commands to SUMA program from script

3

SurfaceMetrics

Provides information on surface mesh

3

SurfMeasures

Compute various measurements for surface or pair of surfaces

3

quickspec

Generate (basic) specification file for running suma

3

@surf_to_vol_spackle

Project values from surface to volume and fill holes

2

@SUMA_Make_Spec_SF

Convert SureFit surfaces to SUMA spec files

1

Surf2VolCoord

1

SurfClust

Find clusters on surfaces

1

SurfDist

Output shortest distance between two nodes on a surface (along surface or Euclidean)

1

SurfDsetInfo

Display information about surface dataset

1

SurfExtrema

Find local extrema in a (surface) dataset

1

SurfFWHM

1

SurfInfo

Show information on surface

1

SurfMesh

Reduce number of points in surface mesh

1

SurfPatch

Extract patch of surface or compute volume from specified nodes

1

SurfQual

Quality check for surfaces

1

SurfRetinoMap

1

SurfSmooth

Smooth surfaces

1

@SurfSmooth.HEAT_07.examples

1

SurfToSurf

Interpolate data from one surface onto mesh of another surface

1

suma_change_spec

1

SUMA_glxdino

1

SUMA_paperplane

1

SUMA_pixmap2eps

1

ROI2dataset

Convert ROI (e.g., after drawing) to SUMA-type dset

1

3dSurfMask

Generate volumetric mask for inside of surface

1

ConvertDset

Converts a surface dataset from one format to another

1

ConvertSurface

Convert surface files among various formats

1

CompareSurfaces

Compute distances between two surfaces at each node

1

CreateIcosahedron

1

MapIcosahedron

Create new version of surface mesh using mesh of icosahedron

1

@IsoMasks

1

MakeColorMap

Make afni and suma colormaps

Mask/skull-strip/segment

5

3dAutomask

Generate a brain and skull-only mask

5

3dSkullStrip

Enhanced skull stripping

5

@SSwarper

Combines skull stripping with generating a warp to a nonlinear template space; directly combinable with afni_proc.py, too!

4

3dmask_tool

for combining/dilating/eroding/filling masks

3

@NoisySkullStrip

Strips the skull of anatomical datasets with low SNR

3

3dSeg

Segment anatomical (t1w) volume into major brain tissue types

1

plugin(Draw Dataset)

Manually draw ROI mask datasets

1

3dinfill

Edit masks by filling in holes

1

3dIntracranial

Strip off outside-the-brain voxels

1

plugin(Gyrus Finder)

Interactively segment gray and white matter

1

3dClipLevel

Find value to threshold off outside-the-brain voxels

Make/edit/evaluate stimulus timing files

4

make_random_timing.py

Generate random stimulus times files

4

timing_tool.py

Edit stimulus timing files

1

1dMarry

Combine ragged 1D files for use with 3dDeconvolve’s -stim_times_AM2 option

1

make_stim_times.py

Convert 0/1 stim file format to stim times format

1

RSFgen

(obsolete -> use make_random_timing.py)

1

@make_stim_file

(obsolete/esoteric/do not use; use what???); make stim files for 3dDeconvolve

1

stimband

Edit dset headers

5

3dinfo

Print out information from the header

5

nifti_tool

Displays, modifies, copies nifti structures in datasets

4

3drefit

Lets you change attributes in a dataset header

3

3dCM

Estimate dset’s center of mass, and allow recentering

2

3dnewid

Assign a new ID code to a dataset (also, generate a random string for filenames); useful for scripting to get temporary filenames/directory names

1

3dAttribute

Print out a single header attribute

1

3dnvals

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

1

3dNotes

Lets you put text notes into a dataset header

1

plugin(Dataset NOTES)

Interactive header notes editor

1

gifti_tool

Displays, modifies, copies nifti structures in datasets

1

cifti_tool

Displays, modifies, copies nifti structures in datasets

1

nifti1_tool

(how diff than nifti_tool???)

1

@AfniOrient2RAImap

Convert orientation code into signed code used in AFNI header

1

@AfniOrientSign

Convert orientation code into signed +/-1 code relative to RAI and permutations

1

@FromRAI

Convert RAI coordinates into another coordinate order

1

@ToRAI

Convert coordinates to RAI order

1

@FullPath

Get absolute path of a file

1

@GetAfniBin

Returns path of afni executables

1

@GetAfniDims

Get dimensions of dataset

1

@GetAfniID

Get AFNI ID of dataset

1

@GetAfniOrient

Get orientation code of dataset

1

@GetAfniPrefix

Get prefix part of dataset name

1

@GetAfniRes

Get voxel resolution of dataset

1

@GetAfniView

Get afni view equivalent of dataset (+orig,+tlrc)

1

@parse_name

Return parts of an AFNI or NIFTI dataset name

1

@parse_afni_name

Return parts of an AFNI dataset name

1

ParseName

Return parts of a dataset name including AFNI specifiers

1

@FindAfniDsetPath

Find a path to dataset

1

@isOblique

Flag if dataset is marked as oblique

1

@Shift_Volume

Move origin of dataset by specified amount or shift between MNI and MNI_ANAT

Compute various numbers from datasets

5

3dFWHMx

Estimate FWHM for all sub-bricks of dataset

3

3dBrickStat

Simple statistics (max, min, mean) for scripts

2

3dExtrema

Find local maxima (or minima) of datasets

1

3ddot

Dot product (correlation coefficient) of 2 sub-bricks

1

3dStatClust

Find statistically connected clusters

1

3dGetrow

Output voxel values for a row/column in x,y,z space

1

3dFWHM

(obsolete -> use 3dFWHMx)

Blur and smooth dsets

5

3dmerge

Process (e.g., blur) and optionally combine datasets

1

3dBlurInMask

Blur a dataset, but only inside a mask (or masks)

1

3dBlurToFWHM

Blur a dataset to a given level of smoothness (for inter-site studies)

1

3danisosmooth

Anisotropic blurring of a dataset (e.g., to clean up structural images)

1

3dMedianFilter

Smooth a 3D volume using a median filter

Volume editing/image processing

4

3dedge3

Calculate edges in 3D

4

3danisosmooth

Smooth a dataset using an anisotropic technique to preserve edges

4

3dUnifize

Correct T1-weighted dataset for non-uniform histogram

2

3dSharpen

3D sharpening filter applied to a dataset (to clean up a template)

1

3dUniformize

(obsolete -> use 3dUnifize)

Update AFNI, install software (not demos)

5

@update.afni.binaries

Update current AFNI binaries

5

afni_system_check.py

Evaluate present setup

4

rPkgsInstall

Get+install all necessary R packages

1

@UpdateAfni

(obsolete -> use @update.afni.binaries)

1

@get.afni.version

Download an archived version of AFNI source code using github

1

afni_vcheck

Check if update needed (compare present and available version numbers)

Simple dset calcs (-> make new dsets)

5

3dcalc

Voxel-by-voxel general purpose calculator

5

3dmerge

Various spatial filters, thresholds, and averaging

5

3dTstat

Various statistics of multi-brick datasets, voxel-by-voxel

4

3dMean

Average datasets together, voxel-by-voxel, for each timept

4

3danisosmooth

Edge preserving filter for spatial smoothing

1

3dWinsor

Nonlinear order statistics filter for spatial smoothing

1

3dLocalstat

Find simple statistical values for neighborhoods around each voxel

1

3dLocalBistat

Compute various bivariate statistics for neighborhoods around each voxel

1

3dLocalstat

Compute some local statistics in a neighborhood around each voxel

1

3dLocalACF

Compute mixed model ACF parameters in a neighborhood around each voxel

1

3dLocalPV

Compute the ‘principal vector’ from a time series dataset, in a neighborhood around each voxel

1

3dLocalSVD

Compute the SVD from a time series dataset, in a neighborhood around each voxel

1

3dLocalHistog

Compute the count of how many times each unique value occurs, in a neighborhood around each voxel

1

3dTto1D

Collapse 4D data to 1D in various ways

1

3dmatcalc

Applies matrix to datasets

1

3dmatmult

Multiply datasets as matrices

Resting state FMRI parameters

3

3dRSFC

Calculate RSFC parameters (ALFF, fALFF, RSFA, etc.) for uncensored time series

3

3dReHo

Calculate ReHo (Kendall’s coefficient of concordance) for time series

3

3dLombScargle

Calculate amp/pow spectrum (like FFT) along time axis with missing time points

3

3dAmpToRSFC

Calculate RSFC parameters (ALFF, fALFF, RSFA, etc.) from 3dLombScargle output

Make/edit correlation matrices

4

3dNetCorr

Calculate correlation matrix of a set of ROIs, as well as WB maps of each

3

fat_mat_sel.py

Visualize functional correlation (*.netcc files) or tracted-WM property (*.grid file) matrices

1

@ROI_Corr_Mat

Make an NxN ROI correlation matrix of N ROIs (consider 3dNetCorr instead)

1

3dErrtsCormat

Compute the correlation matrix for the residual (or error) time series in a dataset

Make/edit ROIs and clusters, resample

5

3dresample

Rewrite dataset, possibly in new orientation, with new voxel size

5

3dClusterize

Find clusters of voxels in a dataset and print out a table about the clusters

4

3dmerge

Edit datasets (e.g., blur, cluster), and optionally combine them

3

3dclust

Find+report about clusters in a dataset (see 3dClusterize for a newer program with newer options and easier syntax)

3

3dUndump

Create a 3D dataset from text data; complements 3dmaskdump

3

3dROIMaker

Threshold and clusterize dataset, as well as inflate (esp. for tractography prep)

2

3dfractionize

Resample a mask to a different grid size

1

3dExtrema

Find local extrema within volumes

1

3dmaxima

Find local extrema within volumes

1

3dClustCount

Apply thresholds to dsets at various levels, and just count clusters of various sizes; used mainly for simulations.

Edit dsets: concatenate, split, add/remove slices

4

3dZeropad

Add zero slices around the edges of a dataset

3

3dZcat

Assemble a 3D+time dataset from multiple input sub-bricks

3

3dAutobox

Automatically crop a dataset to remove empty space

3

3dZcutup

Cut slices out of a dataset to make a ‘thinner’ dataset

3

3dXYZcat

Glue multiple sub-bricks together along the {x|y|z}-axis

1

3dbucket

Assemble a bucket dataset from multiple input sub-bricks3dTcat

1

3dTsplit4D

Convert a 3D+time dataset into multiple 3D single-brick files

1

3dZregrid

Interpolate a dataset to a different slice thickness

Drive AFNI/SUMA, make images/snapshots/montages

5

@chauffeur_afni

Wrapper to combine environment+driving functionality to save image files of 3D dataset (nice in conjunction with 2dcat to form arrays of images)

5

2dcat

Very useful program for making grids of images and things (nice in conjunction with @chauffeur_afni or generally driving AFNI)

5

@snapshot_volreg

Drive AFNI to save QC images of EPI-anatomical alignment

4

DriveSuma

Drive suma from external program

3

@Quiet_Talkers

Close all network talking afni and suma instances (often used at end of “talking” scripts)

3

@djunct_4d_imager

Wrapper to combine environment+driving functionality to save image/movies files of 4D dataset

3

plugout_drive

Drive afni GUI from external program

2

@DriveAfni

Example script to drive afni GUI with class data

2

@DriveSuma

Example script to drive suma with class data

1

HalloSuma

1

adjunct_calc_mont_dims.py

Sub-functionality of @djunct_dwi_selector.tcsh

1

@djunct_dwi_selector.tcsh

Helper/intermediate function for fat_proc_select_vols

1

adjunct_select_str.py

Sub-functionality of @djunct_dwi_selector.tcsh

1

plugout_ijk

1

plugout_tt

1

plugout_tta

1

@snapshot_volreg3

(obsolete -> use @snapshot_volreg)

1

@CommandGlobb

Execute AFNI commands for multiple datasets

1

prompt_popup

Popup a dialog box with a message and buttons

1

prompt_user

(obsolete -> use prompt_popup)

1

@AfniEnv

Get and set AFNI environment variables

1

imcat

(deprecated name -> use new name 2dcat)

Deal with 1D time series

4

1d_tool.py

Perform various manipulations of 1D data

4

1dplot

Graph values from columns in a file

3

1dtranspose

Transpose 1D files (interchange rows and columns)

1

1dCorrelate

Calculate correlation coefficients between 1D columns, with confidence intervals

1

1deval

1D calculator (like 3dcalc for 1D files)

1

1dcat

Catenate 1D files horizontally (use system program cat for vertical combining)

1

1dgrayplot

Show values from columns in a file as bands of gray levels

1

1dmatcalc

Matrix calculator for 1D files

1

1dsum

Add up all numbers in columns of a 1D file (can also do means)

1

1dTsort

Sort each column of the input 1D file (separately)

1

1dsvd

Compute the Singular Value Decomposition of a matrix (including PCA)

1

1dUpsample

Interpolate columns of a 1D file to a finer grid

1

column_cat

Catenate data horizontally

Convert surfaces from other software

5

@SUMA_Make_Spec_FS

Convert output from standard FreeSurfer ‘recon-all’ processing to AFNI+SUMAland

1

@SUMA_Make_Spec_Caret

Convert output from standard Caret processing to AFNI+SUMAland

1

@SUMA_Make_Spec_SF

Convert output from standard SureFit processing to AFNI+SUMAland

1

@SUMA_FSvolToBRIK

1

@SUMA_renumber_FS

Renumber standard FS-‘recon-all’ seg+parc values; make tissue-grouped maps (part of @SUMA_Make_Spec_FS)

1

@suma_reprefixize_spec

1

@FSlabel2dset

1

FSread_annot

1

@FS_roi_label

1

parse_fs_lt_log.py

Parse FreeSurfer region labels to get indices

Convert statistics and p-values

4

ccalc

A command line calculator (like 3dcalc)

4

cdf

Compute probabilities, thresholds for standard distributions

4

p2dsetstat

Convert a p-value to a stat, using parameters stored in a dset header

Compare dset volumes (masks or valued)

5

3dABoverlap

Count overlaps between 2 datasets (union, intersection, etc.)

5

3dSliceNDice

Calculate Dice coefficients slice-by-slice (for all three FOV planes) between mask dsets.

4

3dMatch

Find pairs of similar-looking subbricks between two groups of dsets

1

@DiceMetric

Computes Dice Coefficient between two datasets

1

3ddot

Calculate correlation coefficients between sub-brick pairs in a 4D dset

1

3ddot_beta

Faster version of 3ddot, though currently just for calculating eta-squared

1

3dOverlap

Count of number of voxels that are nonzero in ALL of the input dataset sub-bricks

Time series pre-processing

4

3dTshift

Shift slices to a common time origin (temporal interpolation)

3

3dBrainSync

Alter one dataset’s time series to be maximally correlated with another dataset’s time series

1

3dDespike

Remove spikes from voxel time series

1

3dDetrend

Remove trends from voxel time series

1

3dTproject

Project out time series (like -errts from 3dDeconvolve)

1

3dFourier

FFT-based lowpass and highpass filtering

1

3dTsmooth

Smooth time series in the time domain

1

3dTRfix

Resample a dataset in time from an irregular grid to a regular grid

1

RetroTS.py

Generate slicewise physiological regressors

Time series analysis

5

3dREMLfit

Multiple linear regression (generalized least squares)

4

3dDeconvolve

Multiple linear regression and deconvolution (ordinary least squares)

1

3dNLfim

Nonlinear regression

1

3dLSS

Ad hoc version of IM regression, giving amplitudes for each stimulus event

1

3dTcorrelate

Correlate two input datasets, voxel-by-voxel

1

3dAutoTcorrelate

Correlate each voxel with every other voxel

1

3dpc

Principal component analysis

1

3dDeconvolve_f

(obsolete -> use 3dDeconvolve)

1

3dSynthesize

Compute 3d+time dataset from partial model

1

plugin(Deconvolution)

Interactive deconvolution

1

3ddelay

Single regressor linear analysis with time shifting

1

plugins(Nlfit and Nlerr)

Interactive nonlinear regression

1

3dfim

Linear regression (obsolete -> use 3dDeconvolve)

1

3dfim+

Linear regression (obsolete -> use 3dDeconvolve)

1

1dNLfit

Fit a general model to a vector of data

Quality checks (for 3D+time datasets or results)

4

3dToutcount

Check voxel time series for quality (temporal outliers)

4

@radial_correlate

Check datasets for correlation artifact

4

gen_ss_review_scripts.py

Generate QC review scripts

1

3dTqual

Check dataset sub-bricks for quality (spatial outliers)

1

@compute_gcor

Compute average pairwise correlation (GCOR), one number

1

gen_ss_review_table.py

Generate spread-sheet of review_basic results

1

3dCountSpikes

(obsolete -> use 3dToutcount)

Miscellaneous file manipulations

4

file_tool

Display or edit data in arbitrary files

4

1d_tool.py

For manipulating and evaluating 1D files

1

@diff.files

Compare (diff) a set of files to those in another location

1

@diff.tree

Compare (diff) 2 directory trees of files

1

2swap

Byte pair swap, e.g., ab ba

1

4swap

Byte quad swap, e.g., abc dcba

1

24swap

Mixed 2 and 4 byte swaps in same file

1

strblast

Find a string in a file and replace it with junk

1

@NoExt

Remove specified file extensions from file name

1

@NoPound

Change name of file or dataset to avoid pound (#) symbols

1

@np

Generate new prefix given some base prefix

MVM modelling of (correlational or structural) matrices

3

fat_mvm_prep.py

Combine *.grid/*.netcc files with subject data in CSV files; for fat_mvm* modeling

3

fat_mvm_review.py

(only beta)

3

fat_mvm_scripter.py

Read in a data table file (esp. from fat_mvm_prep.py) and build 3dMVM command

1

fat_lat_csv.py

Make latent variables for CSV file data using factor analysis; esp for fat_mvm* usage

1

fat_mat_sel.py

Plot matrices from 3dNetcorr (*.netcc) or 3dTrackID (*.grid) files

1

fat_mvm_gridconv.py

Convert ooold 3dTrackID output *.grid files; should be unnecessary now

Generate model 1D time series

3

3dDeconvolve

Generate hemodynamic responses for stimulus timing files

1

1dBport

Generate columns of sines and cosines for bandpassing

1

sqwave

Generate a square wave (a very old program)

1

waver

Generate hemodynamic responses to stimulus time series

Dset histograms

3

3dHist

Compute histograms using functions for generating priors

1

3dAnhist

Create and plot histogram of dataset, print peaks

1

3dhistog

Create histogram of dataset to a file

1

plugin(Histogram)

Interactively graphs histogram of a dataset (or ROI)

1

plugin(ScatterPlot)

Interactively graphs 1 sub-brick vs. another (or ROI)

Download/install demos

4

@Install_D99_macaque

Install Saleem D99 macaque atlas and template

4

@Install_DBSproc

Install DBS processing pipeline script

4

@Install_FATCAT_DEMO2

Install newer FATCAT Demo for DTI processing with fat_proc programs (and including TORTOISE and FreeSurfer processing)

3

@Install_FATCAT_DEMO

Install original FATCAT Demo for DTI + some FMRI processing

3

@Install_FATMVM_DEMO

Install FATCAT+MVM statistical modeling demo, multivariate modeling in conjuction with tractography (also applies to correlation matrices such as from 3dNetCorr)

1

@Install_3dPFM_Demo

1

@Install_AfniRetinoDemo

1

@Install_ClustScat_Demo

1

@Install_InstaCorr_Demo

Install demo data for InstaCorr, instant correlation

1

@Install_MEICA_Demo

1

@Install_NIH_Marmoset

Install NIH Marmoset atlas and template

1

@Install_RSFMRI_Motion_Group_Demo

1

@Install_TSrestMovieDemo

DICOM info and conversion

5

Dimon

Read DICOM files on disk or as they are created

5

dcm2niix_afni

Primary choice for converting DCM files of DWI dsets (and possibly FMRI)

3

dicom_hinfo

Print out selected information from a number of DICOM headers

2

to3d

Read image files, write AFNI format datasets (not usually directly used)

2

from3d

Write dataset slices into image files

1

dicom_hdr

Print out information from one DICOM header

1

dicom_to_raw

For extracting only the binary image data from a DICOM file

1

@move.to.series.dirs

Partition DICOM images into run directectories

1

Ifile

Read GE realtime EPI files and runs to3d

1

Imon

(obs - use Dimon); Read GE realtime EPI files as they are created

1

rtfeedme

Dissect one dataset, sends images to AFNI realtime plugin

1

plugin(RT Options)

Control options for AFNI realtime image input

1

abut

Create zero-filled slices to put into dataset gaps

1

dicom_hdr

Print information from a DICOM file

1

ge_header

Print information from a GE I. file

1

mayo_analyze

Print information froman ANALYZE .hdr file

1

siemens_vision

Print information from a Siemens Vision .ima file

1

Dimon1

(obsolete -> use Dimon)

Copy/convert/manipulate dsets

5

3dcopy

Copy a dataset to make new files

3

3dThreetoRGB

Convert 3 scalar datasets to 1 RGB AFNI format dataset

1

3dBRAIN_VOYAGERtoAFNI

1

3dAFNIto3D

Read image files, write AFNI format datasets

1

3dAFNItoANALYZE

Convert AFNI format dataset to ANALYZE format

1

3dAFNItoMINC

Convert AFNI format dataset to MINC format

1

3dMINCtoAFNI

Convert MINC format dataset to AFNI format

1

3dAFNItoNIFTI

1

3dAFNItoNIML

1

3dAFNItoRaw

1

3dANALYZEtoAFNI

(obsolete -> use 3dcopy or to3d)

1

3dCRUISEtoAFNI

1

3dPAR2AFNI.pl

(almost useless helpfile… obsolete???)

1

3drename

Rename dataset files

1

3ddup

Make an ‘empty’ duplicate (warp-on-demand) of a dataset

1

3dTwotoComplex

Create complex dataset from two sub-bricks

1

3dEmpty

Create header file only for specified dimensions

1

3dVecRGB_to_HSL

Convert RGB coloration to HSL values; typically intermed step in viewing prob. tracking results.

1

3dMaskToASCII

Changing dset spatial structure

5

3dresample

Rewrite dataset in new orientation, with new voxel size

4

fat_proc_axialize_anat

Rotate brain to have standard viewing planes along slices

3

3dLRflip

Flip dataset contents Left <-> Right

1

3daxialize

Rewrite dataset with slices in different direction

Change dset temporal structure

1

3dUpsample

Upsample in time (to a shorter TR)

Supplementary/open programs included in AFNI

1

cjpeg

Compress an image file to a JPEG file

1

djpeg

Decompress a JPEG file to an image file

1

mpeg_encode

Convert sequence of images into MPEG movie

1

whirlgif

Concatenate series of GIFs into a single one

Supplemental/underlying programs (no desc needed)

1

@global_parse

1

lib_afni1D.py

1

afni_util.py

1

3dToyProg

Simulate/generate dsets

1

3dTSgen

Generate 3D+time dataset from 1D model and noise

1

3dClustSim

Simulate datasets and estimate statistical power

1

slow_surf_clustsim.py

Like 3dClustSim, but for surface data.

1

quick.alpha.vals.py

Companion to slow_surf_clustsim.py

1

3dConvolve

Simulate datasets via convolution (for testing 3dDeconvolve)

1

3dInvFMRI

Compute stimulus time series given activation map and 3D+time dataset

1

3dDTtoNoisyDWI

Make a simulated DWI set with random noise, from DT+gradient information

1

1dgenARMA11

Generate synthetic ARMA(1,1) correlated time series, to test 3dREMLfit

Miscellaneous visualization tools

3

aiv

AFNI Image Viewer program

3

3dGrayplot

Take a 3D+time dataset and make a summary 2D image for data quality review

1

plugin(Render[new])

Interactive volume rendering

1

plugin(Dataset#N)

Graph extra dataset time series in AFNI graph viewer

1

afni_open

Open various AFNI/SUMA files (*.xmat, *.pdf, etc.)

Miscellaneous utilities

5

apsearch

Simple+approx string searching; used in atlases and helps

4

count

Generate numbered strings for command line scripts

4

afni_history

Display a log of updates to AFNI code

3

ccalc

A command line calculator (like 3dcalc)

3

cdf

Compute probabilities, thresholds for standard distributions

2

@xyz_to_ijk

calculate (i, j, k) indices in a volume from (x, y, z) coordinates

1

byteorder

Report the byteorder of the current CPU

Unclassed

1

1dAstrip

1

@1dDiffMag

1

1ddot

1

1dfft

1

1dFlagMotion

1

1dgrayplot

1

1dnorm

1

@2dwarper

1

@2dwarper.Allin

1

2perm

1

3dAcost

1

3dbuc2fim

1

3dClipLevel

1

3dConformist

1

3dDegreeCentrality

1

3dECM

1

3dEntropy

1

3dGenFeatureDist

1

3dGenPriors

1

3dkmeans

1

3dLFCD

1

3dmaskSVD

1

3dMSE

1

3dMultiThresh

1

3dnoise

1

3dnvals

1

3dPFM

1

3dPolyfit

1

3dproject

1

3dretroicor

1

3dSignatures

1

3dSpaceTimeCorr

1

3dSpatNorm

1

3dStatClust

1

3dsvm

1

3dsvm_linpredict

1

3dTnorm

1

3dtoXdataset

1

3dXClustSim

1

@4Daverage

1

@afni.run.me

1

afni_skeleton.py

1

AnalyzeTrace

1

balloon

1

BrainSkin

1

@build_afni_Xlib

1

@Center_Distance

1

@CheckForAfniDset

1

@clean_help_dir

1

@clip_volume

1

ConvexHull

1

@DeblankFileNames

1

demo.fixed.niml.do

1

demo.mobile.niml.do

1

@demo_prompt

1

@DO.examples

1

eg_main_chrono.py

1

@ElectroGrid

1

ent16

1

@escape-

1

@ExamineGenFeatDists

1

ExamineXmat

1

@fast_roi

1

FD2

1

fdrval

1

fftest

1

fim2

1

@fix_FSsphere

1

@float_fix

1

float_scan

1

ftosh

1

gen_epi_review.py

1

GLTsymtest

1

gui_uber_align_test.py

1

gui_uber_skel.py

1

gui_uber_subj.py

1

gui_uber_ttest.py

1

gui_xmat.py

1

@help.AFNI

1

help_format

1

im2niml

1

images_equal

1

imand

1

imaver

1

imcalc

1

imcutup

1

imdump

1

immask

1

imreg

1

imrotate

1

imstack

1

imstat

1

imupsam

1

inspec

1

@make_plug_diff

1

make_pq_script.py

1

meica.py

1

module_test_lib.py

1

mritopgm

1

mycat

1

myget

1

neuro_deconvolve.py

1

nicat

1

niccc

1

nifti1_test

1

niml_feedme

1

niprobe

1

nsize

1

option_list.py

1

@Purify_1D

1

python_module_test.py

1

qdelaunay

1

qhull

1

quotize

1

rbox

1

read_matlab_files.py

1

realtime_receiver.py

1

rmz

1

ROIgrow

1

rotcom

1

SampBias

1

ScaleToMap

1

@ScaleVolume

1

@ScriptCheck

1

serial_helper

1

sfim

1

@simulate_motion

1

@SkullStrip_TouchUp

1

SpharmDeco

1

@Spharm.examples

1

@statauxcode

1

@T1scale

1

tfim

1

@TimeDiff

1

tokens

1

uber_skel.py

1

uber_ttest.py

1

ui_xmat.py

1

uniq_images

1

@VolCenter

1

xmat_tool.py

1

Xphace

R programs (in R; called by others)

1

1dGC.R

1

1dRplot

1

1dRplot.R

1

1dSVAR.R

1

3dAOV.R

1

3dGC.R

1

3dICA.R

1

3dICC.R

1

3dICC_REML.R

1

3dKS.R

1

3dMEMA.R

1

3dPFM.R

1

3dRetinoPhase

1

3dRowFillin

1

3dRprogDemo

1

3dRprogDemo.R

1

3dSignatures.R

1

AFNI_Batch_R

1

AFNIplot.R

1

afni_run_R

1

@ANATICOR

1

@DoPerRoi.py

1

ExamineXmat.R

1

FIRdesign

1

Level2.R

1

@RenamePanga

1

@Reorder

1

@RetinoProc

1

@R_funclist

1

@ShowDynamicRange

1

Signatures.R

1

smooth.R

1

SpharmReco