3. All program helps

This is a list of all AFNI programs. Click on any name to see the help for that program.

For additional reference, please also see the “classified” list of helps HERE, where programs are loosely grouped by topic and functionality, with a brief description of each provided.

1dApar2mat

1dAstrip

1dBandpass

1dBport

1dCorrelate

1dDW_Grad_o_Mat

1dDW_Grad_o_Mat++

1dFlagMotion

1dMarry

1dNLfit

1dRplot

1dSEM

1dTsort

1dUpsample

1d_tool.py

1dcat

1ddot

1deval

1dfft

1dgenARMA11

1dgrayplot

1dmatcalc

1dnorm

1dplot

1dplot.py

1dsound

1dsum

1dsvd

1dtranspose

24swap

2dImReg

2dcat

2perm

2swap

3dABoverlap

3dAFNIto3D

3dAFNItoANALYZE

3dAFNItoMINC

3dAFNItoNIFTI

3dAFNItoNIML

3dAFNItoRaw

3dANALYZEtoAFNI

3dANOVA

3dANOVA2

3dANOVA3

3dAcost

3dAllineate

3dAmpToRSFC

3dAnatNudge

3dAnhist

3dAttribute

3dAutoTcorrelate

3dAutobox

3dAutomask

3dBRAIN_VOYAGERtoAFNI

3dBallMatch

3dBandpass

3dBlurInMask

3dBlurToFWHM

3dBrainSync

3dBrickStat

3dCM

3dCRUISEtoAFNI

3dClipLevel

3dClustCount

3dClustSim

3dClusterize

3dCompareAffine

3dConformist

3dConvolve

3dCountSpikes

3dDFT

3dDTeig

3dDTtoDWI

3dDTtoNoisyDWI

3dDWItoDT

3dDWUncert

3dDeconvolve

3dDeconvolve_f

3dDegreeCentrality

3dDespike

3dDetrend

3dECM

3dEigsToDT

3dEmpty

3dEntropy

3dErrtsCormat

3dExchange

3dExtractGroupInCorr

3dExtrema

3dFDR

3dFFT

3dFWHM

3dFWHMx

3dFourier

3dFriedman

3dGenFeatureDist

3dGenPriors

3dGetrow

3dGrayplot

3dGroupInCorr

3dHist

3dICC

3dISC

3dIntracranial

3dInvFMRI

3dKruskalWallis

3dLFCD

3dLME

3dLMEr

3dLRflip

3dLSS

3dLocalACF

3dLocalBistat

3dLocalHistog

3dLocalPV

3dLocalSVD

3dLocalstat

3dLombScargle

3dMEMA

3dMEPFM

3dMINCtoAFNI

3dMSE

3dMSS

3dMVM

3dMVM_validator

3dMannWhitney

3dMaskToASCII

3dMatch

3dMax

3dMean

3dMedianFilter

3dMultiThresh

3dNLfim

3dNetCorr

3dNormalityTest

3dNotes

3dNwarpAdjust

3dNwarpApply

3dNwarpCalc

3dNwarpCat

3dNwarpFuncs

3dNwarpXYZ

3dOverlap

3dPAR2AFNI.pl

3dPFM

3dPVmap

3dPeriodogram

3dPolyfit

3dProbTrackID

3dPval

3dQwarp

3dREMLfit

3dROIMaker

3dROIstats

3dRSFC

3dRank

3dRankizer

3dReHo

3dRegAna

3dRetinoPhase

3dRowFillin

3dRprogDemo

3dSeg

3dSetupGroupInCorr

3dSharpen

3dSignatures

3dSkullStrip

3dSliceNDice

3dSpaceTimeCorr

3dSpatNorm

3dStatClust

3dSurf2Vol

3dSurfMask

3dSynthesize

3dTORTOISEtoHere

3dTRfix

3dTSgen

3dTagalign

3dTcat

3dTcorr1D

3dTcorrMap

3dTcorrelate

3dTfilter

3dTfitter

3dThreetoRGB

3dTnorm

3dToutcount

3dToyProg

3dTproject

3dTqual

3dTrackID

3dTshift

3dTsmooth

3dTsort

3dTsplit4D

3dTstat

3dTto1D

3dTwotoComplex

3dUndump

3dUnifize

3dUniformize

3dUpsample

3dVecRGB_to_HSL

3dVol2Surf

3dWarp

3dWarpDrive

3dWavelets

3dWilcoxon

3dWinsor

3dXClustSim

3dXYZcat

3dZcat

3dZcutup

3dZeropad

3dZipperZapper

3dZregrid

3danisosmooth

3daxialize

3dbuc2fim

3dbucket

3dcalc

3dclust

3dcopy

3ddelay

3ddot

3ddot_beta

3ddup

3dedge3

3dfim

3dfim+

3dfractionize

3dhistog

3dinfill

3dinfo

3dkmeans

3dmaskSVD

3dmask_tool

3dmaskave

3dmaskdump

3dmatcalc

3dmatmult

3dmaxima

3dmerge

3dnewid

3dnoise

3dnvals

3dpc

3dproject

3drefit

3drename

3dresample

3dretroicor

3drotate

3dsvm

3dsvm_linpredict

3dtoXdataset

3dttest

3dttest++

3dvolreg

4swap

@1dDiffMag

@2dwarper

@2dwarper.Allin

@4Daverage

@ANATICOR

@AddEdge

@AfniEnv

@AfniOrient2RAImap

@AfniOrientSign

@Align_Centers

@Atlasize

@Center_Distance

@CheckForAfniDset

@ClustExp_CatLab

@ClustExp_run_shiny

@CommandGlobb

@DO.examples

@DTI_studio_reposition

@DeblankFileNames

@DiceMetric

@DoPerRoi.py

@DriveAfni

@DriveSuma

@ElectroGrid

@ExamineGenFeatDists

@FS_roi_label

@FSlabel2dset

@FindAfniDsetPath

@FromRAI

@FullPath

@GetAfniBin

@GetAfniDims

@GetAfniID

@GetAfniOrient

@GetAfniPrefix

@GetAfniRes

@GetAfniView

@GradFlipTest

@Install_3dPFM_Demo

@Install_AfniRetinoDemo

@Install_ClustScat_Demo

@Install_D99_macaque

@Install_DBSproc

@Install_FATCAT_DEMO

@Install_FATCAT_DEMO2

@Install_FATMVM_DEMO

@Install_IBT_DATASETS

@Install_InstaCorr_Demo

@Install_MACAQUE_DEMO

@Install_MACAQUE_DEMO_REST

@Install_MEICA_Demo

@Install_NIH_Marmoset

@Install_NMT

@Install_RSFMRI_Motion_Group_Demo

@Install_TSrestMovieDemo

@IsoMasks

@MakeLabelTable

@NoExt

@NoPound

@NoisySkullStrip

@Purify_1D

@Quiet_Talkers

@ROI_Corr_Mat

@ROI_decluster

@ROI_modal_grow

@R_funclist

@RenamePanga

@Reorder

@RetinoProc

@SSwarper

@SUMA_AlignToExperiment

@SUMA_FSvolToBRIK

@SUMA_Make_Spec_Caret

@SUMA_Make_Spec_FS

@SUMA_Make_Spec_SF

@SUMA_renumber_FS

@ScaleVolume

@ScriptCheck

@Shift_Volume

@ShowDynamicRange

@SkullStrip_TouchUp

@Spharm.examples

@SurfSmooth.HEAT_07.examples

@T1scale

@TimeDiff

@ToRAI

@UpdateAfni

@VolCenter

@afni.run.me

@afni_R_package_install

@afni_refacer_make_master

@afni_refacer_make_master_addendum

@afni_refacer_make_onebigA12

@afni_refacer_run

@align_partial_oblique

@animal_warper

@auto_align

@auto_tlrc

@build_afni_Xlib

@chauffeur_afni

@clean_help_dir

@clip_volume

@compute_OC_weights

@compute_gcor

@demo_prompt

@diff.files

@diff.tree

@djunct_4d_imager

@djunct_4d_slices_to_3d_vol

@djunct_anonymize

@djunct_calc_mont_dims.py

@djunct_combine_str.py

@djunct_dwi_selector.tcsh

@djunct_edgy_align_check

@djunct_glue_imgs_vert

@djunct_is_label.py

@djunct_json_value.py

@djunct_make_script_and_rst.py

@djunct_modal_smoothing_with_rep

@djunct_montage_coordinator

@djunct_overlap_check

@djunct_select_str.py

@djunct_slice_space

@djunct_ssw_intermed_edge_imgs

@djunct_vol_3slice_select

@escape-

@extract_meica_ortvec

@fast_roi

@fat_tract_colorize

@fix_FSsphere

@float_fix

@get.afni.version

@global_parse

@grayplot

@help.AFNI

@isOblique

@make_plug_diff

@make_stim_file

@measure_bb_thick

@measure_erosion_thick

@measure_in2out

@move.to.series.dirs

@np

@parse_afni_name

@parse_name

@radial_correlate

@simulate_motion

@snapshot_volreg

@snapshot_volreg3

@statauxcode

@suma_acknowledge

@suma_reprefixize_spec

@surf_to_vol_spackle

@thickness_master

@toMNI_Awarp

@toMNI_Qwarpar

@update.afni.binaries

@xyz_to_ijk

AFNI_Batch_R

AlphaSim

AnalyzeTrace

BayesianGroupAna.py

BrainSkin

CA_EZ_atlas.csh

ClustExp_HistTable.py

ClustExp_StatParse.py

CompareSurfaces

ConvertDset

ConvertSurface

ConvexHull

CreateIcosahedron

DTIStudioFibertoSegments

Dimon

Dimon1

DoPerRoi.py

DriveSuma

ExamineXmat

FATCAT_matplot

FD2

FIRdesign

FSread_annot

GLTsymtest

HalloSuma

Ifile

InstaTract

IsoSurface

MBA

MakeColorMap

MapIcosahedron

PTA

ParseName

RBA

ROI2dataset

ROIgrow

RSFgen

RetroTS.py

SUMA_glxdino

SUMA_paperplane

SUMA_pixmap2eps

SampBias

ScaleToMap

SpharmDeco

SpharmReco

Surf2VolCoord

SurfClust

SurfDist

SurfDsetInfo

SurfExtrema

SurfFWHM

SurfInfo

SurfMeasures

SurfMesh

SurfPatch

SurfQual

SurfRetinoMap

SurfSmooth

SurfToSurf

SurfaceMetrics

TRR

Vecwarp

Xphace

abids_json_info.py

abids_json_tool.py

abids_tool.py

abut

adjunct_apqc_tsnr_general

adjunct_apqc_tsnr_no_mask

adjunct_apqc_tsnr_with_mask

adjunct_aw_tableize_roi_info.py

adjunct_calc_mont_dims.py

adjunct_combine_str.py

adjunct_is_label.py

adjunct_make_script_and_rst.py

adjunct_select_str.py

adjunct_simplify_cost.py

adjunct_suma_fs_mask_and_qc

adjunct_suma_fs_qc.tcsh

adjunct_suma_fs_roi_info

adjunct_suma_fs_rois.tcsh

adjunct_tort_plot_dp_align

adjunct_tort_read_dp_align.py

adwarp

afni

afni_check_omp

afni_history

afni_open

afni_proc.py

afni_python_wrapper.py

afni_restproc.py

afni_run_R

afni_skeleton.py

afni_system_check.py

afni_vcheck

aiv

align_epi_anat.py

ap_run_simple_rest.tcsh

apqc_make_html.py

apqc_make_tcsh.py

apsearch

auto_warp.py

balloon

byteorder

cat_matvec

ccalc

cdf

check_dset_for_fs.py

cifti_tool

cjpeg

column_cat

convert_cdiflist_to_grads.py

count

dcm2niix_afni

demoExpt.py

dicom_hdr

dicom_hinfo

dicom_to_raw

djpeg

dsetstat2p

eg_main_chrono.py

ent16

epi_b0_correct.py

fat_lat_csv.py

fat_mat2d_plot.py

fat_mat_sel.py

fat_mat_tableize.py

fat_mvm_gridconv.py

fat_mvm_prep.py

fat_mvm_review.py

fat_mvm_scripter.py

fat_proc_align_anat_pair

fat_proc_axialize_anat

fat_proc_connec_vis

fat_proc_convert_dcm_anat

fat_proc_convert_dcm_dwis

fat_proc_decmap

fat_proc_dwi_to_dt

fat_proc_filter_dwis

fat_proc_grad_plot

fat_proc_imit2w_from_t1w

fat_proc_map_to_dti

fat_proc_select_vols

fat_roi_row.py

fdrval

fftest

file_tool

fim2

float_scan

from3d

ftosh

ge_header

gen_epi_review.py

gen_group_command.py

gen_ss_review_scripts.py

gen_ss_review_table.py

get_afni_model_PRF

get_afni_model_PRF_6

get_afni_model_PRF_6_BAD

gifti_tool

help_format

im2niml

images_equal

imand

imaver

imcalc

imcat

imcutup

imdump

immask

imreg

imrotate

imstack

imstat

imupsam

inspec

lpc_align.py

make_latest_tgz.csh

make_pq_script.py

make_random_timing.py

make_stim_times.py

map_TrackID

mayo_analyze

meica.py

mpeg_encode

mritopgm

mycat

myget

neuro_deconvolve.py

nicat

niccc

nifti1_test

nifti1_tool

nifti_tool

niml_feedme

niprobe

nsize

p2dsetstat

parse_fs_lt_log.py

plugout_drive

plugout_ijk

plugout_tt

plugout_tta

prompt_popup

prompt_user

python_module_test.py

quick.alpha.vals.py

quickspec

quotize

rPkgsInstall

rbox

read_matlab_files.py

realtime_receiver.py

rmz

rotcom

rtfeedme

serial_helper

sfim

siemens_vision

slow_surf_clustsim.py

sqwave

stimband

strblast

suma

suma_change_spec

tedana_wrapper.py

tfim

timing_tool.py

to3d

tokens

uber_align_test.py

uber_proc.py

uber_skel.py

uber_subject.py

uber_ttest.py

unWarpEPI.py

uniq_images

waver

whereami

whirlgif

xmat_tool.py