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 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 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 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 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 @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_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
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 abids_json_info.py abids_json_tool.py
abids_tool.py 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
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 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_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