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 1dXmatTool 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 Sat Oct 31 02:00:40 AM EDT 2026 — RWCox