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 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 3dClusterize 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
3dIntracranial 3dInvFMRI 3dKruskalWallis
3dLFCD 3dLME 3dLRflip
3dLSS 3dLocalACF 3dLocalBistat
3dLocalHistog 3dLocalPV 3dLocalSVD
3dLocalstat 3dLombScargle 3dMEMA
3dMEPFM 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 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_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 @afni_refacer_make_master
@afni_refacer_make_onebigA12 @afni_refacer_run @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_4d_slices_to_3d_vol @djunct_calc_mont_dims.py @djunct_combine_str.py
@djunct_dwi_selector.tcsh @djunct_edgy_align_check @djunct_is_label.py
@djunct_json_value.py @djunct_make_script_and_rst.py @djunct_montage_coordinator
@djunct_select_str.py @djunct_slice_space @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_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
DriveSuma ExamineXmat FATCAT_matplot
FD2 FIRdesign FSread_annot
GLTsymtest HalloSuma Ifile
InstaTract IsoSurface MBA
MakeColorMap MapIcosahedron 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
Vecwarp Xphace abids_json_info.py
abids_json_tool.py abids_tool.py abut
adwarp afni afni_check_omp
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 apqc_make_html.py
apqc_make_tcsh.py apsearch auto_warp.py
balloon byteorder cat_matvec
ccalc cdf cifti_tool
cjpeg column_cat count
dcm2niix_afni demoExpt.py 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
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