2.8. 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”.


2.8.1. 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

2.8.2. 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 (and see 3dLMEr)

5

3dLMEr

Voxelwise Linear Mixed-Effects (LME) modeling. The linear mixed-effects modeling approach implemented in 3dLMEr is for population-level analysis, and is much more flexible than 3dLME.

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

4

3dICC

Compute voxelwise IntraClass correlation (ICC) values. ICC computations are performed with one of the three types: ICC(1, 1), ICC(2,1) and ICC(3,1). Input can be either effect estimates only or effect estimates plus their t-statistics.

4

3dISC

Compute voxelwise InterSubject Correlation (ISC). ISCs are assessed for naturalistic data at the population through linear mixed-effects (LME) modeling.

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

3

3dTfitter

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

3

3dPFM

Deconvolution analysis of fMRI voxel time series with L1 norm methods (LASSO, Dantzig Selector), akin to 3dTfitter but using a different procedure and algorithms

3

3dMEPFM

Deconvolution analysis of multi-echo fMRI voxel time series with L1 norm methods (LASSO), akin to 3dPFM

2

3dSpaceTimeCorr

Calculate the following for 2 dsets on the same grid: for each voxel in grid, calculate correlation map in each dset, and then correlate those spatial maps; store that correlation value at that location. A way to look at similarity of correlation across, say, resting state datasets, perhaps.

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

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

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

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

2.8.3. 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

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

2.8.4. Build FMRI pipelines

5

afni_proc.py

Generate tcsh script for full processing (including QC) of single subject FMRI data— it might just be your new best friend

4

gen_ss_review_scripts.py

Generate QC review scripts

4

@afni_refacer_run

Award-winning program to help anonymize datasets by defacing and/or refacing them (with free QC images!)

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)

2

apqc_make_tcsh.py

Program used by afni_proc.py to build QC HTML (this builds script to generate images+text)

2

apqc_make_html.py

Program used by afni_proc.py to build QC HTML (this builds HTML pieces made by apqc_make_tcsh.py)

1

uber_proc.py

2.8.5. 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

@SSwarper

Skull-stripping program that uses a reference anatomical

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

afni_proc.py

Can wrap many registration operations (in addition to/as part of its FMRI processing pipeline generation)

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

@animal_warper

alignment and skullstripping and moves atlas regions to native space, specially suited for animal brains

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

3

cat_matvec

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

3

epi_b0_correct.py

Performs B0 distortion correction along the phase encode (PE) direction, using an acquired frequency (phase) image; originally written by Vinai Roopchansingh

2

3dCompareAffine

Measure the “distance” between 2 different affine spatial transformation matrices, for potential use in testing alignment software tools run in different environments

2

1dApar2mat

Compute an affine spatial transformation matrix from the set of parameters output by ‘3dAllineate -1Dparam_save …’. This code can be used to modify the matrix by altering the physically relevant parameters (e.g., scalings, shifts, rotations, shears), and could be combined with program cat_matvec, for example.

1

auto_warp.py

wrapper for nonlinear warping with 3dQwarp

1

@auto_tlrc

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

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

@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

3drotate

Rigid body rotation of dataset in 3D

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

@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

1

plugin(Edit Tagset)

Place ‘tags’ in a dataset interactively

2.8.6. 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

2.8.7. 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

4

@afni_refacer_run

Award-winning program to help anonymize datasets by defacing and/or refacing them (with free QC images!)

4

@animal_warper

alignment and skullstripping and moves atlas regions to native space, specially suited for animal brains (and directly combinable with afni_proc.py)

3

@NoisySkullStrip

Strips the skull of anatomical datasets with low SNR

3

3dSeg

Segment anatomical (t1w) volume into major brain tissue types

1

3dinfill

Edit masks by filling in holes

1

3dIntracranial

Strip off outside-the-brain voxels

1

3dClipLevel

Find value to threshold off outside-the-brain voxels

1

plugin(Draw Dataset)

Manually draw ROI mask datasets

1

plugin(Gyrus Finder)

Interactively segment gray and white matter

2.8.8. 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

stimband

2.8.9. 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

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

1

plugin(Dataset NOTES)

Interactive header notes editor

2.8.10. 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

2.8.11. 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

2.8.12. 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)

2.8.13. Update AFNI, install software, check setup/info (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

4

@afni_R_package_install

Install the R packages required by some AFNI programs from the Linux terminal (see also rPkgsInstall).

3

afni_check_omp

Returns one value, the number of OMP_NUM_THREADS set (for programs able to use multiple CPUs with OpenMP)

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)

2.8.14. 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

2

3dPVmap

Compute the first 2 principal vectors (component time series) of a 3D+time dataset, then output a dataset measuring the R^2 of the input dataset with the 2D subspace spanned by these 2 vectors. The same algorithm is used in the 3dGrayplot program to order the voxels to cluster similar time series together, for visualization.

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

2.8.15. 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

2

3dSpaceTimeCorr

Calculate the following for 2 dsets on the same grid: for each voxel in grid, calculate correlation map in each dset, and then correlate those spatial maps; store that correlation value at that location. A way to look at similarity of correlation across, say, resting state datasets, perhaps.

2.8.16. Region-wise group analysis

5

RBA

Region-Based Analysis. RBA performs Bayesian multilevel (BML) modeling for a list of predefined ROIs. Instead of controlling for multiple testing in conventional population-level analysis, RBA borrows and calibrates the information across regions (see also BayesianGroupAna.py)

5

BayesianGroupAna.py

The Python version of RBA, for Bayesian multilevel (BML) modeling for a list of predefined ROIs (see also RBA)

3

MBA

Matrix-Based Analysis. MBA is for population-level analysis with matrix (e.g., correlation) data from each subject as input. Partial pooling is adopted through Bayesian multilevel (BML) modeling

2.8.17. Make/edit correlation matrices

4

3dNetCorr

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

3

fat_mat2d_plot.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

fat_mat_sel.py

(obsolete -> use fat_mat2d_plot.py)

1

3dErrtsCormat

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

2.8.18. 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)

3

3dExchange

Exchange values from one set of indices with another set

2

3dfractionize

Resample a mask to a different grid size

2

@ROI_modal_grow

Dilate regions iteratively by most common value within a neighborhod

2

@ROI_decluster

Remove small separate parts of region

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.

2.8.19. Edit dsets: concatenate, split, add/remove slices

4

3dTcat

Concatenate sub-bricks from input datasets into one big 3D+time dataset

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-bricks

1

3dTsplit4D

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

1

3dZregrid

Interpolate a dataset to a different slice thickness

2.8.20. 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

@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)

2.8.21. Deal with 1D time series

4

1d_tool.py

Perform various manipulations of 1D data

4

1dplot

Plot/graph values from columns in a file

4

1dplot.py

Like 1dplot, but more modern Python-based viewing (more options; requires Python-matplotlib)

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

2.8.23. 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

2.8.24. 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 (complement of dsetstat2p)

3

dsetstat2p

Convert a stat to a p-value, using parameters stored in a dset header (complement of p2dsetstat)

2.8.25. 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

2.8.26. 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

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

2.8.27. 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

3dSynthesize

Compute 3d+time dataset from partial model

1

3ddelay

Single regressor linear analysis with time shifting

1

3dfim+

Linear regression (obsolete -> use 3dDeconvolve)

1

1dNLfit

Fit a general model to a vector of data

1

plugin(Deconvolution)

Interactive deconvolution

1

plugins(Nlfit and Nlerr)

Interactive nonlinear regression

2.8.28. 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

2.8.29. 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

2.8.30. MVM modelling of (correlational or structural) matrices

3

fat_mat2d_plot.py

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

3

fat_mvm_prep.py

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

3

fat_mvm_scripter.py

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

1

fat_mat_sel.py

(obsolete -> use fat_mat2d_plot.py)

1

fat_mvm_gridconv.py

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

2.8.31. Interact with multi-echo data

5

afni_proc.py

Generate FMRI processing pipelines, including for multi-echo FMRI data; can use several methods for combining echoes, such as optimally combined (via @compute_OC_weights) and tedana.py, as well as others

3

3dMEPFM

Deconvolution analysis of multi-echo fMRI voxel time series with L1 norm methods (LASSO), akin to 3dPFM

2

@compute_OC_weights

Compute optimally combined weights dataset

1

meica.py

P Kundu’s MEICA denoising tools

1

@Install_MEICA_Demo

Install the demo archive for P Kundu’s MEICA denoising tools

2.8.32. 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

waver

Generate hemodynamic responses to stimulus time series

2.8.34. 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)

2.8.35. 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_IBT_DATASETS

Install India Brain Templates (IBTs) and atlases (IBTAs), reference volumes across most of human life span for Indian population studies

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)

3

@Install_MACAQUE_DEMO

Install processing examples for task-based FMRI of macaque data, using @animal_warper and afni_proc.py (1 subject)

3

@Install_MACAQUE_DEMO_REST

Install processing examples for resting state FMRI of macaque data, using @animal_warper and afni_proc.py (6 subjects)

3

@Install_NMT

Install NIMH Macaque Template (NMT) datasets (ver=2 is most recent) and CHARM and D99 atlases; can get both symmetric and asymmetric variants.

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

Install the demo archive for P Kundu’s MEICA denoising tools

1

@Install_NIH_Marmoset

Install NIH Marmoset atlas and template

1

@Install_RSFMRI_Motion_Group_Demo

1

@Install_TSrestMovieDemo

2.8.36. 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

rtfeedme

Dissect one dataset, sends images to AFNI realtime plugin

1

dicom_hdr

Print information from a DICOM file

1

Imon

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

1

plugin(RT Options)

Control options for AFNI realtime image input

2.8.37. 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

3dAFNItoNIFTI

1

3dAFNItoNIML

1

3dAFNItoRaw

1

3dCRUISEtoAFNI

1

3dPAR2AFNI.pl

(almost useless helpfile… obsolete???)

1

3drename

Rename dataset files

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

2.8.38. 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

2.8.39. Change dset temporal structure

1

3dUpsample

Upsample in time (to a shorter TR)

2.8.40. 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

whirlgif

Concatenate series of GIFs into a single one

1

mpeg_encode

Convert sequence of images into MPEG movie

2.8.42. 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

2.8.43. 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

afni_open

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

1

plugin(Render[new])

Interactive volume rendering

1

plugin(Dataset#N)

Graph extra dataset time series in AFNI graph viewer

2.8.44. 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

1

1dsound

Create an audio file from a 1D file (= columns of numbers in ASCII format); fun but not very useful

2.8.45. 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

3dClipLevel

1

3dConformist

1

3dDegreeCentrality

1

3dECM

1

3dEntropy

1

3dGenFeatureDist

1

3dGenPriors

1

3dkmeans

1

3dLFCD

1

3dmaskSVD

1

3dMSE

1

3dMultiThresh

1

3dnvals

1

3dPolyfit

1

3dretroicor

1

3dSignatures

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_prompt

1

@DO.examples

1

eg_main_chrono.py

1

@ElectroGrid

1

@escape-

1

@ExamineGenFeatDists

1

ExamineXmat

1

@fast_roi

1

@ShowDynamicRange

1

fdrval

1

fftest

1

fim2

1

@fix_FSsphere

1

@float_fix

1

float_scan

1

gen_epi_review.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

mycat

1

myget

1

neuro_deconvolve.py

1

nicat

1

niccc

1

niml_feedme

1

niprobe

1

nsize

1

@Purify_1D

1

python_module_test.py

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

SpharmReco

1

@Spharm.examples

1

@statauxcode

1

@T1scale

1

tfim

1

@TimeDiff

1

tokens

1

uber_skel.py

1

uber_ttest.py

1

uniq_images

1

@VolCenter

1

xmat_tool.py

1

@Reorder

1

@RenamePanga

1

3dRetinoPhase

1

@ANATICOR

1

@RetinoProc

1

qdelaunay

1

qhull

2.8.46. Retired (no longer in the build)

0

3dAFNItoMINC

Convert AFNI format dataset to MINC format (MINC now extinct)

0

3dMINCtoAFNI

Convert MINC format dataset to AFNI format (MINC now extinct)

0

AlphaSim

(obsolete -> used 3dClustSim)

0

3dFWHM

(obsolete -> use 3dFWHMx)

0

3dMax

(obsolete -> use 3dBrickStat)

0

@auto_align

(obsolete -> use align_epi_anat.py or 3dAllineate)

0

@UpdateAfni

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

0

3dANALYZEtoAFNI

(obsolete -> use 3dcopy or to3d)

0

Dimon1

(obsolete -> use Dimon)

0

3dCountSpikes

(obsolete -> use 3dToutcount)

0

3dfim

(obsolete -> use 3dDeconvolve)

0

3dUniformize

(obsolete -> use 3dUnifize)

0

@DTI_studio_reposition

(probably obsolete)

0

@make_stim_file

(obsolete -> use timing_tool.py)

0

3dICC_REML.R

(obsolete -> use 3dICC)

0

3dAOV.R

(obsolete -> use 3dMVM)

0

lpc_align.py

(obsolete -> use align_epi_anat.py or 3dAllineate)

0

afni_restproc.py

(obsolete -> use afni_proc.py)

0

@snapshot_volreg3

(obsolete -> use @snapshot_volreg)

0

1dDW_Grad_o_Mat

(obsolete -> use 1dDW_Grad_o_Mat++)

0

3dProbTrackID

(obsolete -> use 3dTrackID)

0

3dFourier

(obsolete -> use 3dBandpass)

0

3dttest

(obsolete -> use 3dttest++; for “3dttest -base ..” functionality, use “3dttest++ -singletonA ..”)

0

3dAnatNudge

(obsolete -> use align_epi_anat.py, 3dAllineate or Nudge plugin)

0

3ddup

(obsolete -> use 3dcopy or something else to make new dset)

0

3dDeconvolve_f

(obsolete -> use 3dDeconvolve)

0

DoPerRoi.py

0

3dbuc2fim

0

3dnoise

0

3dproject

0

3dWavelets

0

abut

Create zero-filled slices to put into dataset gaps

0

ent16

0

ftosh

0

ge_header

Print information from a GE I. file

0

Ifile

Read GE realtime EPI files and runs to3d

0

check_dset_for_fs.py

not needed

0

mayo_analyze

Print information from an ANALYZE .hdr file

0

mritopgm

0

siemens_vision

Print information from a Siemens Vision .ima file

0

sqwave

Generate a square wave (a very old program)

0

Xphace

0

FD2

0

fat_lat_csv.py

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

0

fat_mvm_review.py

(only beta)

0

fat_proc_grad_plot

(to be) replaced by newer version

2.8.47. R programs (in R; called by others)

0

1dGC.R

0

1dRplot

0

1dRplot.R

0

1dSVAR.R

0

3dGC.R

0

3dICA.R

0

3dICC.R

0

3dKS.R

0

3dMEMA.R

0

3dPFM.R

0

3dRowFillin

0

3dRprogDemo

0

3dRprogDemo.R

0

3dSignatures.R

0

AFNI_Batch_R

0

AFNIplot.R

0

afni_run_R

0

ExamineXmat.R

0

FIRdesign

0

Level2.R

0

@R_funclist

0

Signatures.R

0

smooth.R