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.

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	1dsum
1dsvd	1dtranspose	24swap
2dImReg	2perm	2swap
3dABoverlap	3dAFNIto3D	3dAFNItoANALYZE
3dAFNItoMINC	3dAFNItoNIFTI	3dAFNItoNIML
3dAFNItoRaw	3dANALYZEtoAFNI	3dANOVA
3dANOVA2	3dANOVA3	3dAcost
3dAllineate	3dAmpToRSFC	3dAnatNudge
3dAnhist	3dAttribute	3dAutoTcorrelate
3dAutobox	3dAutomask	3dBRAIN_VOYAGERtoAFNI
3dBandpass	3dBlurInMask	3dBlurToFWHM
3dBrainSync	3dBrickStat	3dCM
3dCRUISEtoAFNI	3dClipLevel	3dClustCount
3dClustSim	3dConformist	3dConvolve
3dCountSpikes	3dDFT	3dDTeig
3dDTtoDWI	3dDTtoNoisyDWI	3dDWItoDT
3dDWUncert	3dDeconvolve	3dDeconvolve_f
3dDegreeCentrality	3dDespike	3dDetrend
3dECM	3dEigsToDT	3dEmpty
3dEntropy	3dErrtsCormat	3dExtractGroupInCorr
3dExtrema	3dFDR	3dFFT
3dFWHM	3dFWHMx	3dFourier
3dFriedman	3dGenFeatureDist	3dGenPriors
3dGetrow	3dGroupInCorr	3dHist
3dIntracranial	3dInvFMRI	3dKruskalWallis
3dLFCD	3dLME	3dLRflip
3dLSS	3dLocalACF	3dLocalBistat
3dLocalHistog	3dLocalPV	3dLocalSVD
3dLocalstat	3dLombScargle	3dMEMA
3dMINCtoAFNI	3dMSE	3dMVM
3dMVM_validator	3dMannWhitney	3dMaskToASCII
3dMatch	3dMax	3dMean
3dMedianFilter	3dMultiThresh	3dNLfim
3dNetCorr	3dNormalityTest	3dNotes
3dNwarpAdjust	3dNwarpApply	3dNwarpCalc
3dNwarpCat	3dNwarpFuncs	3dNwarpXYZ
3dOverlap	3dPAR2AFNI.pl	3dPFM
3dPeriodogram	3dPolyfit	3dProbTrackID
3dPval	3dQwarp	3dREMLfit
3dROIMaker	3dROIstats	3dRSFC
3dRank	3dRankizer	3dReHo
3dRegAna	3dRetinoPhase	3dRowFillin
3dRprogDemo	3dSeg	3dSetupGroupInCorr
3dSharpen	3dSignatures	3dSkullStrip
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_InstaCorr_Demo	@Install_MEICA_Demo	@Install_NIH_Marmoset
@Install_RSFMRI_Motion_Group_Demo	@Install_TSrestMovieDemo	@IsoMasks
@MakeLabelTable	@NoExt	@NoPound
@NoisySkullStrip	@Purify_1D	@Quiet_Talkers
@ROI_Corr_Mat	@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	@align_partial_oblique
@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_calc_mont_dims.py	@djunct_combine_str.py	@djunct_dwi_selector.bash
@djunct_select_str.py	@escape-	@fast_roi
@fat_tract_colorize	@fix_FSsphere	@float_fix
@get.afni.version	@global_parse	@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_reprefixize_spec	@thickness_master	@toMNI_Awarp
@toMNI_Qwarpar	@update.afni.binaries	AFNI_Batch_R
AlphaSim	AnalyzeTrace	BrainSkin
ClustExp_HistTable.py	ClustExp_StatParse.py	CompareSurfaces
ConvertDset	ConvertSurface	ConvexHull
CreateIcosahedron	DTIStudioFibertoSegments	Dimon
Dimon1	DriveSuma	ExamineXmat
FATCAT_matplot	FD2	FIRdesign
FSread_annot	GLTsymtest	HalloSuma
Ifile	InstaTract	IsoSurface
MakeColorMap	MapIcosahedron	ParseName
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	Vecwarp
Xphace	abut	adwarp
afni	afni_history	afni_open
afni_proc.py	afni_restproc.py	afni_run_R
afni_skeleton.py	afni_system_check.py	afni_util.py
afni_vcheck	aiv	align_epi_anat.py
apsearch	auto_warp.py	balloon
byteorder	cat_matvec	ccalc
cdf	cifti_tool	cjpeg
column_cat	count	dcm2niix_afni
dicom_hdr	dicom_hinfo	dicom_to_raw
djpeg	eg_main_chrono.py	ent16
fat_lat_csv.py	fat_mat_sel.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	gifti_tool	help_format
im2niml	images_equal	imand
imaver	imcalc	imcat
imcutup	imdump	immask
imreg	imrotate	imstack
imstat	imupsam	inspec
lpc_align.py	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	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