2.5. 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”.

2.5.1. 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

2.5.2. 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
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

2.5.3. 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 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

2.5.4. 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)

2.5.5. 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 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

2.5.6. 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

2.5.7. 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
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

2.5.8. 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 @make_stim_file (obsolete/esoteric/do not use; use what???); make stim files for 3dDeconvolve
1 stimband  

2.5.9. 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 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

2.5.10. 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
1 3dFWHM (obsolete -> use 3dFWHMx)

2.5.11. 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

2.5.12. 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)
1 3dUniformize (obsolete -> use 3dUnifize)

2.5.13. 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)

2.5.14. 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
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

2.5.15. 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

2.5.16. 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

2.5.17. 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.

2.5.18. 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

2.5.19. 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 imcat to form arrays of images)
5 imcat 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 @djunct_calc_mont_dims.py Sub-functionality of @djunct_dwi_selector.bash
1 @djunct_dwi_selector.bash Helper/intermediate function for fat_proc_select_vols
1 @djunct_select_str.py Sub-functionality of @djunct_dwi_selector.bash
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

2.5.20. 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

2.5.22. 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_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

2.5.23. 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

2.5.24. 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

2.5.25. 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

2.5.26. 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

2.5.27. 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)

2.5.28. 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

2.5.29. 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

2.5.30. 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

2.5.32. 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)

2.5.33. 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  

2.5.34. 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)

2.5.35. 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 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 3dAFNItoNIML  
1 3dAFNItoRaw  
1 3dANALYZEtoAFNI (obsolete -> use 3dcopy or to3d)
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  

2.5.36. 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

2.5.37. Change dset temporal structure

1 3dUpsample Upsample in time (to a shorter TR)

2.5.38. 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

2.5.40. 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

2.5.41. 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.)

2.5.42. 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

2.5.43. 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  

2.5.44. 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 @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