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
3dICC 3dISC 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_MACAQUE_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
@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_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_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 check_dset_for_fs.py cifti_tool
cjpeg column_cat 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_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 xmat_tool.py