4.2. 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”.

4.2.1. 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

4.2.2. 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

4.2.3. 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

4.2.4. 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

4.2.5. 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

4.2.6. 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

4.2.7. 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

4.2.8. 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

4.2.9. 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

4.2.10. 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

4.2.11. 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	Smooth a dataset using an anisotropic technique to preferentially preserve edges (e.g., to clean up structural images)
1	3dMedianFilter	Smooth a 3D volume using a median filter

4.2.12. Volume editing/image processing

4	3dedge3	Calculate edges in 3D, using “Optimal edge detection using recursive filtering”
4	3danisosmooth	Smooth a dataset using an anisotropic technique to preferentially preserve edges (e.g., to clean up structural images)
4	3dUnifize	Correct T1-weighted dataset for non-uniform histogram
2	3dSharpen	3D sharpening filter applied to a dataset (to clean up a template)

4.2.13. 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)

4.2.14. 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	Smooth a dataset using an anisotropic technique to preferentially preserve edges (e.g., to clean up structural images)
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

4.2.15. 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.

4.2.16. 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

4.2.17. 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

4.2.18. 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.

4.2.19. 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

4.2.20. 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)

4.2.21. 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

4.2.22. DWI/DTI/diffusion-related

5	3dDWItoDT	Estimate diffusion tensor and parameters from DWIs (and see fat_proc_dwi_to_dt)
5	3dTrackID	Perform deterministic, mini- or fully-probabilistic tracking for DTI or HARDI data
5	fat_proc_convert_dcm_anat	Wrapper to convert 3D dataset from DICOMs, with additional nice features.
5	fat_proc_convert_dcm_dwis	Wrapper to convert 4D dataset from DICOMs, with additional nice features.
5	fat_proc_decmap	Make a directionally-encoded color map of DTI data.
5	fat_proc_dwi_to_dt	Wrapper to estimate DT and parameters, and align datasets.
5	fat_proc_filter_dwis	Graphical interface to help user select out bad volumes (esp. from DWI dataset)
5	fat_proc_imit2w_from_t1w	Invert a T1w dataset to imitate a T2w-type contrast dset (as a backup ref for DWI processing with TORTOISE)
5	fat_proc_map_to_dti	Wrapper to bring data (esp. FS surfaces and parcels) into DTI space
5	fat_proc_select_vols	Select out good valumes in a DWI dataset + associated text files
5	@GradFlipTest	Test what ‘flip’, if any, is necessary for gradients in a DWI set
5	1dDW_Grad_o_Mat++	Perform calculations and conversions of DWI gradients and matrices
4	3dDWUncert	Estimate uncertainty of FA and V1 of diffusion tensor dataset, for tracking purposes (and see fat_proc_dwi_to_dt)
4	@fat_tract_colorize	Visualize volumetric output maps from 3dTrackID tracking
3	fat_roi_row.py	Select a single ROI’s row out of a connectivity matrix file (*.grid or *.netcc)
3	3dZipperZapper	Try to see if volumes (particularly DWI volumes) have dropout or severe motion; mostly stable, but somewhat in beta
3	fat_proc_connec_vis	View volumetric output (WM connections/segments) from tractography, esp. the “3dTrackID -dump_rois ..” output.
2	convert_cdiflist_to_grads.py	Convert of GE cdiflist to a more usable form (gradient file + file of b-values);
1	3dDTeig	Computes eigenvalues and eigenvectors for an input DT set
1	3dDTtoDWI	Calculate ‘ideal’ DWIs for each grad, from DT+b0+gradient files
1	3dDTtoNoisyDWI	Make a simulated DWI set with random noise, from DT+gradient information
1	3dEigsToDT	Calculate diffusion tensor dataset from eigenvalues and eigenvectors
1	3dTORTOISEtoHere	Convert standard TORTOISE-format DTs to AFNI-format DTs
1	DTIStudioFibertoSegments	Convert a DTIStudio Fiber file to a SUMA segment file
1	InstaTract	(intermediate function only)
1	map_TrackID	Apply linear affine transform to track file (*.trk format only)

4.2.23. 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

4.2.24. 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)

4.2.25. 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

4.2.26. 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

4.2.27. 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

4.2.28. 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

4.2.29. 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

4.2.30. 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

4.2.31. 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

4.2.32. 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

4.2.33. Fourier related, time series/freq

4	3dDFT	FFT along time axis
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
3	3dBandpass
3	3dRSFC	Calculate RSFC parameters (ALFF, fALFF, RSFA, etc.) for uncensored time series
1	3dFFT	FFT along spatial axis
1	1dBandpass
1	3dPeriodogram
1	stimband

4.2.34. Dset histograms

3	3dHist	Compute histograms using functions for generating priors
1	3dAnhist	Create and plot histogram of dataset, print peaks (output is a list of peaks in the histogram, to stdout)
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)

4.2.35. 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

4.2.36. DICOM info and conversion

5	Dimon	Read DICOM files on disk or as they are created (i.e., can monitor real-time acquisition of DICOM image files)
5	dcm2niix_afni	Another choice for converting DCM files (particularly useful for DWI dsets, often)
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

4.2.37. 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

4.2.38. 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

4.2.39. Change dset temporal structure

1

3dUpsample

Upsample in time (to a shorter TR)

4.2.40. Supplementary/open programs included in AFNI

1	cjpeg	Compress an image file to a JPEG file, with various control options for type upsampling/downsampling, etc.
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

4.2.41. Supplemental/underlying programs (no desc needed)

1	@global_parse
1	3dToyProg
1	@djunct_4d_slices_to_3d_vol
1	@djunct_anonymize
1	@djunct_edgy_align_check
1	@djunct_glue_imgs_vert
1	@djunct_json_value.py
1	@djunct_modal_smoothing_with_rep
1	@djunct_montage_coordinator
1	@djunct_slice_space
1	@djunct_ssw_intermed_edge_imgs
1	@djunct_vol_3slice_select
1	adjunct_simplify_cost.py
1	adjunct_combine_str.py
1	adjunct_is_label.py
1	adjunct_make_script_and_rst.py
1	@suma_acknowledge
1	@afni_refacer_make_master
1	@afni_refacer_make_master_addendum
1	@afni_refacer_make_onebigA12

4.2.42. Simulate/generate dsets

1	3dTSgen	Generate 3D+time dataset from 1D model and noise; the time series for each voxel is generated according to a user specified signal+noise model.
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

4.2.43. Miscellaneous visualization tools

3	aiv	AFNI Image Viewer program; shows 2D images from the command line in an AFNI-like image viewer, and can also read images in NIML format
3	3dGrayplot	Take a 3D+time dataset and make a summary 2D image for data quality review; can organize and scale in different ways
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

4.2.44. 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

4.2.45. 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

4.2.46. 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

4.2.47. R programs (written in R; called by other programss)

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