AFNI program -help files

Results of running each program with the -help option

* All -help Files on One VERY Long Page *       * Common options for most AFNI programs *

** Interactive AFNI Help (afni -help) **       * Unix Environment Variables and AFNI *

* Detailed History of AFNI software changes *       * AFNI and OpenMP *

** Documentation Page from Gang Chen **       ** PDF handouts from AFNI Workshops **

** Faces of AFNI Users **

Links in the Table Below are to Individual -help Files
[The notation a indicates an archaic program, kept for compatibility]
1dApar2mat 1dAstrip 1dBandpass 1dBport
1dcat 1dCorrelate @1dDiffMag 1ddot
1dDW_Grad_o_Mat++ 1deval 1dfft 1dFlagMotion
1dgenARMA11 1dgrayplot 1dMarry 1dmatcalc
1dNLfit 1dnorm 1dplot 1dplot.py
1dRplot 1dSEM 1dsound 1dsum
1dsvd 1d_tool.py 1dtranspose 1dTrdm
1dTsort 1dUpsample 24swap a 2dcat
2dImReg @2dwarper.Allin 2perm 2swap a
3dABoverlap 3dAFNIto3D 3dAFNItoANALYZE a 3dAFNItoNIFTI
3dAFNItoNIML 3dAFNItoRaw 3dAllineate 3dAmpToRSFC
3dAnhist a 3danisosmooth 3dANOVA 3dANOVA2
3dANOVA3 3dAttribute 3dAutobox 3dAutomask
3dAutoTcorrelate 3daxialize a 3dBallMatch 3dBandpass
3dBlurInMask 3dBlurToFWHM 3dBrainSync 3dBRAIN_VOYAGERtoAFNI
3dBrickStat 3dbucket 3dcalc 3dClipLevel a
3dclust 3dClustCount 3dClusterize 3dClustSim
3dCM 3dCompareAffine 3dConformist 3dConvolve
3dcopy 3dCRUISEtoAFNI 3dDeconvolve 3dDegreeCentrality
3ddelay 3dDepthMap 3dDespike 3dDetrend
3dDFT 3dDiff 3ddot a 3ddot_beta
3dDTeig 3dDTtoDWI 3dDTtoNoisyDWI 3dDWItoDT
3dDWUncert 3dECM 3dedge3 3dedgedog
3dEdu_01_scale 3dEigsToDT 3dEmpty 3dEntropy
3dExchange 3dExtractGroupInCorr 3dExtrema 3dFDR
3dFFT 3dfim+ 3dfractionize 3dFriedman
3dFWHMx 3dGenFeatureDist 3dGenPriors 3dGetrow
3dGLMM 3dGrayplot 3dGroupInCorr 3dHist
3dhistog 3dICC 3dinfill 3dinfo
3dIntracranial a 3dInvFMRI 3dISC 3dkmeans
3dKruskalWallis 3dLFCD 3dLME 3dLME2
3dLMEr 3dLocalACF 3dLocalBistat 3dLocalHistog
3dLocalPV 3dLocalstat 3dLocalSVD 3dLocalUnifize
3dLombScargle 3dLRflip 3dLSS 3dMannWhitney
3dmaskave 3dmaskdump 3dmaskSVD 3dMaskToASCII
3dmask_tool 3dmatcalc 3dMatch 3dmatmult
3dmaxdisp 3dmaxima 3dMean 3dMedianFilter
3dMEMA 3dMEPFM 3dmerge 3dMSE
3dMSS 3dMultiThresh 3dMVM 3dMVM_validator
3dNetCorr 3dnewid 3dNLfim 3dNormalityTest
3dNotes 3dnvals 3dNwarpAdjust 3dNwarpApply
3dNwarpCalc 3dNwarpCat 3dNwarpFuncs 3dNwarpXYZ
3dOverlap 3dPAR2AFNI.pl 3dpc 3dPeriodogram
3dPFM 3dPolyfit 3dPval 3dPVmap
3dQwarp 3dRank 3dRankizer 3drefit
3dRegAna 3dReHo 3dREMLfit 3drename
3dresample 3dRetinoPhase 3dretroicor 3dROIMaker
3dROIstats 3drotate 3dRowFillin 3dRprogDemo
3dRSA 3dRSFC 3dSeg 3dSetupGroupInCorr
3dSharpen 3dShuffle 3dSignatures 3dSkullStrip
3dSliceNDice 3dSpaceTimeCorr 3dSpaceTimeCorr2 3dStatClust
3dSurf2Vol 3dSurfMask 3dsvm 3dsvm_linpredict
3dSynthesize 3dTagalign 3dTcat 3dTcorr1D
3dTcorrelate 3dTcorrMap 3dTfilter 3dTfitter
3dThreetoRGB 3dTnorm 3dTORTOISEtoHere 3dToutcount
3dtoXdataset 3dToyProg 3dTproject 3dTqual
3dTrackID 3dTRfix 3dTSgen 3dTshift
3dTsmooth 3dTsort 3dTsplit4D 3dTstat
3dttest++ 3dTto1D 3dTwotoComplex 3dUndump
3dUnifize 3dUpsample 3dVecRGB_to_HSL 3dVol2Surf
3dvolreg 3dWarp a 3dWarpDrive a 3dWilcoxon
3dWinsor 3dXClustSim 3dXYZcat 3dZcat
3dZcutup 3dZeropad 3dZipperZapper 3dZregrid
@4Daverage 4swap a abids_json_info.py abids_json_tool.py
abids_tool.py @AddEdge adjunct_apqc_tsnr_general adjunct_atlas_points_to_labeltable
adjunct_aw_tableize_roi_info.py adjunct_calc_mont_dims.py adjunct_cbar_out adjunct_combine_str.py
adjunct_deob_around_origin adjunct_is_label.py adjunct_make_script_and_rst.py adjunct_middle_pair_mask
adjunct_refacer_make_master_addendum2 adjunct_select_str.py adjunct_simplify_cost.py adjunct_suma_fs_mask_and_qc
adjunct_suma_fs_roi_info adjunct_tort_plot_dp_align adjunct_tort_read_dp_align.py adwarp
afni afni_check_omp @AfniEnv afni_history
afni_open @AfniOrient2RAImap afni_proc.py afni_python_wrapper.py
afni_refacer2 @afni_refacer_make_master @afni_refacer_make_master_addendum @afni_refacer_make_onebigA12
@afni_refacer_run @afni_R_package_install @afni.run.me afni_skeleton.py
afni_system_check.py afni_vcheck aiv @Align_Centers
align_epi_anat.py @align_partial_oblique AnalyzeTrace @ANATICOR
@animal_warper apqc_make_html.py apqc_make_tcsh.py ap_run_simple_rest_me.tcsh
ap_run_simple_rest.tcsh apsearch asymm_report.csh @Atlasize
@auto_tlrc auto_warp.py balloon BayesianGroupAna.py
bayes_view BrainSkin build_afni.py @build_afni_Xlib
byteorder cat_matvec ccalc cdf
@Center_Distance @chauffeur_afni chauffeur_map_rois @CheckForAfniDset
cifti_tool cjpeg @clean_help_dir @clip_volume
@ClustExp_CatLab ClustExp_HistTable.py @ClustExp_run_shiny ClustExp_StatParse.py
colorbar_tool.py column_cat @CommandGlobb CompareSurfaces
@compute_gcor @compute_OC_weights compute_ROI_stats.tcsh convert_cdiflist_to_grads.py
ConvertDset ConvertSurface ConvexHull count
count_afni CreateIcosahedron dcm2niix_afni @DeblankFileNames
desphinxify @DiceMetric dicom_hdr dicom_hinfo
dicom_to_raw @diff.files @diff.tree Dimon
djpeg @djunct_4d_imager @djunct_4d_slices_to_3d_vol @djunct_anonymize
@djunct_dwi_selector.tcsh @djunct_edgy_align_check @djunct_glue_imgs_vert @djunct_json_value.py
@djunct_modal_smoothing_with_rep @djunct_montage_coordinator @djunct_overlap_check @djunct_slice_space
@djunct_ssw_intermed_edge_imgs @djunct_vol_3slice_select @DO.examples DriveSuma
dsetstat2p DTIStudioFibertoSegments eg_main_chrono.py @ElectroGrid
epi_b0_correct.py @ExamineGenFeatDists ExamineXmat @extract_meica_ortvec
@fast_roi FATCAT_matplot fat_mat2d_plot.py fat_mat_sel.py
fat_mat_tableize.py fat_mvm_gridconv.py fat_mvm_prep.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_imit2w_from_t1w fat_proc_map_to_dti fat_proc_select_vols fat_roi_row.py
@fat_tract_colorize fdrval file_tool find_variance_lines.tcsh
FIRdesign @fix_FSsphere @float_fix float_scan
from3d a @FromRAI @FSlabel2dset FSread_annot
@FS_roi_label @FullPath gen_cluster_table gen_cluster_table.py
gen_epi_review.py gen_group_command.py gen_ss_review_scripts.py gen_ss_review_table.py
@GetAfniBin @GetAfniDims @GetAfniID get_afni_model_PRF
get_afni_model_PRF_6 get_afni_model_PRF_6_BAD get_afni_model_PRF_DN @GetAfniOrient
@GetAfniPrefix @GetAfniRes @get.afni.version @GetAfniView
gifti_tool @global_parse GLTsymtest @GradFlipTest
@grayplot gtkyd_check gtkyd_check.py HalloSuma
@help.AFNI im2niml a images_equal imand a
imaver a imcalc a imcat a imcutup a
imdump a immask a imreg a imrotate a
imstack a imstat a imupsam a init_user_dotfiles.py
inspec @Install_3dPFM_Demo @Install_AfniRetinoDemo @Install_APMULTI_Demo1_rest
@Install_APMULTI_Demo2_realtime install_bootcamp_data.tcsh @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_MBM_Marmoset @Install_MEICA_Demo @Install_NIH_Marmoset @Install_NMT
@Install_RAT_DEMO_REST @Install_RSFMRI_Motion_Group_Demo @Install_SAM_marmoset @Install_SURFLAYERS_DEMO1
@Install_TSrestMovieDemo InstaTract @isOblique @IsoMasks
IsoSurface lesion_align libgslcblas.so.0 libgsl.so.27
MakeColorMap @MakeLabelTable @make_plug_diff make_pq_script.py
make_random_timing.py make_stim_times.py map_ap_to_deriv.py MapIcosahedron
map_TrackID MBA @measure_bb_thick @measure_erosion_thick
@measure_in2out meica.py @move.to.series.dirs mycat
neuro_deconvolve.py nifti1_tool nifti_tool niml_feedme
niprobe @NoExt @NoisySkullStrip @NoPound
@np nsize a obliquity_remover.py open_apqc.py
p2dsetstat @parse_afni_name parse_fs_lt_log.py ParseName
@parse_name physio_calc.py plugout_drive plugout_ijk
plugout_tt prompt_popup prompt_user PTA
@Purify_1D python_module_test.py quick.alpha.vals.py quickspec
quickspecSL @Quiet_Talkers quotize @radial_correlate
RBA read_matlab_files.py realtime_receiver.py @RenamePanga a
@Reorder @RetinoProc RetroTS.py @R_funclist
ROI2dataset @ROI_Corr_Mat @ROI_decluster ROIgrow
@ROI_modal_grow roi_stats_warnings.py rotcom rPkgsInstall
RSFgen rtfeedme SampBias ScaleToMap
@ScaleVolume @ScriptCheck serial_helper @Shift_Volume
@ShowDynamicRange @simulate_motion @SkullStrip_TouchUp slow_surf_clustsim.py
@snapshot_volreg SpharmDeco @Spharm.examples SpharmReco
@SSwarper sswarper2 stimband stouffer
strblast a suma @suma_acknowledge @SUMA_AlignToExperiment
suma_change_spec @SUMA_FSvolToBRIK @SUMA_Make_Spec_Caret @SUMA_Make_Spec_FS
@SUMA_Make_Spec_SF @SUMA_renumber_FS @suma_reprefixize_spec Surf2VolCoord
SurfaceMetrics SurfClust SurfClustSim SurfDist
SurfDsetInfo SurfExtrema SurfFWHM SurfInfo
SurfLayers SurfLocalstat SurfMeasures SurfMesh
SurfPatch SurfQual SurfRetinoMap SurfSmooth
@SurfSmooth.HEAT_07.examples SurfToSurf @surf_to_vol_spackle @T1scale
tedana_wrapper.py test_afni_prog_help.tcsh @thickness_master @TimeDiff
timing_tool.py to3d tokens @toMNI_Awarp
@toMNI_Qwarpar @ToRAI TRR uber_align_test.py
uber_skel.py uber_subject.py uber_ttest.py uniq_images
unWarpEPI.py @update.afni.binaries Vecwarp @VolCenter
waver a whereami whereami_afni whirlgif
xmat_tool.py @xyz_to_ijk
README.3dsvm.realtime README.afnigui README.atlas_building README.attributes
README.bzip2 README.changes README.compression README.copyright
README.driver README.environment README.func_types README.Ifile
README.notes README.permtest README.plugouts README.realtime
README.registration README.render_scripts README.roi README.setup
README.texlike README.volreg README.web README.ziad
AFNI.changes.dglen AFNI.changes.rickr AFNI.afnirc AFNI.Xdefaults
This page auto-generated on Sat Sep 19 10:07:22 PM EDT 2026 — RWCox