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
3dInSync 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 Fri Oct 9 07:58:45 PM EDT 2026 — RWCox