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
1dCorrelate 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 a 2dImReg 2dcat 2perm
2swap a 3dABoverlap 3dAFNIto3D 3dAFNItoANALYZE a
3dAFNItoNIFTI 3dAFNItoNIML 3dAFNItoRaw 3dANOVA
3dANOVA2 3dANOVA3 3dAllineate 3dAmpToRSFC
3dAnhist a 3dAttribute 3dAutoTcorrelate 3dAutobox
3dAutomask 3dBRAIN_VOYAGERtoAFNI 3dBallMatch 3dBandpass
3dBlurInMask 3dBlurToFWHM 3dBrainSync 3dBrickStat
3dCM 3dCRUISEtoAFNI 3dClipLevel a 3dClustCount
3dClustSim 3dClusterize 3dCompareAffine 3dConformist
3dConvolve 3dDFT 3dDTeig 3dDTtoDWI
3dDTtoNoisyDWI 3dDWItoDT 3dDWUncert 3dDeconvolve
3dDegreeCentrality 3dDepthMap 3dDespike 3dDetrend
3dDiff 3dECM 3dEdu_01_scale 3dEigsToDT
3dEmpty 3dEntropy 3dExchange 3dExtractGroupInCorr
3dExtrema 3dFDR 3dFFT 3dFWHMx
3dFriedman 3dGenFeatureDist 3dGenPriors 3dGetrow
3dGrayplot 3dGroupInCorr 3dHist 3dICC
3dISC 3dIntracranial a 3dInvFMRI 3dKruskalWallis
3dLFCD 3dLME 3dLME2 3dLMEr
3dLRflip 3dLSS 3dLocalACF 3dLocalBistat
3dLocalHistog 3dLocalPV 3dLocalSVD 3dLocalUnifize
3dLocalstat 3dLombScargle 3dMEMA 3dMEPFM
3dMSE 3dMSS 3dMVM 3dMVM_validator
3dMannWhitney 3dMaskToASCII 3dMatch 3dMean
3dMedianFilter 3dMultiThresh 3dNLfim 3dNetCorr
3dNormalityTest 3dNotes 3dNwarpAdjust 3dNwarpApply
3dNwarpCalc 3dNwarpCat 3dNwarpFuncs 3dNwarpXYZ
3dOverlap 3dPAR2AFNI.pl 3dPFM 3dPVmap
3dPeriodogram 3dPolyfit 3dPval 3dQwarp
3dREMLfit 3dROIMaker 3dROIstats 3dRSFC
3dRank 3dRankizer 3dReHo 3dRegAna
3dRetinoPhase 3dRowFillin 3dRprogDemo 3dSeg
3dSetupGroupInCorr 3dSharpen 3dSignatures 3dSkullStrip
3dSliceNDice 3dSpaceTimeCorr 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
3dUpsample 3dVecRGB_to_HSL 3dVol2Surf 3dWarp a
3dWarpDrive a 3dWilcoxon 3dWinsor 3dXClustSim
3dXYZcat 3dZcat 3dZcutup 3dZeropad
3dZipperZapper 3dZregrid 3danisosmooth 3daxialize a
3dbucket 3dcalc 3dclust 3dcopy
3ddelay 3ddot a 3ddot_beta 3dedge3
3dedgedog 3dfim+ 3dfractionize 3dhistog
3dinfill 3dinfo 3dkmeans 3dmaskSVD
3dmask_tool 3dmaskave 3dmaskdump 3dmatcalc
3dmatmult 3dmaxdisp 3dmaxima 3dmerge
3dnewid 3dnvals 3dpc 3drefit
3drename 3dresample 3dretroicor 3drotate
3dsvm 3dsvm_linpredict 3dtoXdataset 3dttest++
3dvolreg 4swap a @1dDiffMag @2dwarper.Allin
@4Daverage @ANATICOR @AddEdge @AfniEnv
@AfniOrient2RAImap @Align_Centers @Atlasize @Center_Distance
@CheckForAfniDset @ClustExp_CatLab @ClustExp_run_shiny @CommandGlobb
@DO.examples @DeblankFileNames @DiceMetric @ElectroGrid
@ExamineGenFeatDists @FS_roi_label @FSlabel2dset @FromRAI
@FullPath @GetAfniBin @GetAfniDims @GetAfniID
@GetAfniOrient @GetAfniPrefix @GetAfniRes @GetAfniView
@GradFlipTest @Install_3dPFM_Demo @Install_APMULTI_Demo1_rest @Install_APMULTI_Demo2_realtime
@Install_AfniRetinoDemo @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
@IsoMasks @MakeLabelTable @NoExt @NoPound
@NoisySkullStrip @Purify_1D @Quiet_Talkers @ROI_Corr_Mat
@ROI_decluster @ROI_modal_grow @R_funclist @RenamePanga a
@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 @VolCenter
@afni.run.me @afni_R_package_install @afni_refacer_make_master @afni_refacer_make_master_addendum
@afni_refacer_make_onebigA12 @afni_refacer_run @align_partial_oblique @animal_warper
@auto_tlrc @build_afni_Xlib @chauffeur_afni @clean_help_dir
@clip_volume @compute_OC_weights @compute_gcor @diff.files
@diff.tree @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 @extract_meica_ortvec @fast_roi
@fat_tract_colorize @fix_FSsphere @float_fix @get.afni.version
@global_parse @grayplot @help.AFNI @isOblique
@make_plug_diff @measure_bb_thick @measure_erosion_thick @measure_in2out
@move.to.series.dirs @np @parse_afni_name @parse_name
@radial_correlate @simulate_motion @snapshot_volreg @suma_acknowledge
@suma_reprefixize_spec @surf_to_vol_spackle @thickness_master @toMNI_Awarp
@toMNI_Qwarpar @update.afni.binaries @xyz_to_ijk AnalyzeTrace
BayesianGroupAna.py BrainSkin ClustExp_HistTable.py ClustExp_StatParse.py
CompareSurfaces ConvertDset ConvertSurface ConvexHull
CreateIcosahedron DTIStudioFibertoSegments Dimon DriveSuma
ExamineXmat FATCAT_matplot FIRdesign FSread_annot
GLTsymtest HalloSuma InstaTract IsoSurface
MBA MakeColorMap MapIcosahedron PTA
ParseName RBA ROI2dataset ROIgrow
RSFgen RetroTS.py SampBias ScaleToMap
SpharmDeco SpharmReco Surf2VolCoord SurfClust
SurfDist SurfDsetInfo SurfExtrema SurfFWHM
SurfInfo SurfLayers SurfLocalstat SurfMeasures
SurfMesh SurfPatch SurfQual SurfRetinoMap
SurfSmooth SurfToSurf SurfaceMetrics TRR
Vecwarp abids_json_info.py abids_json_tool.py abids_tool.py
adjunct_apqc_tsnr_general adjunct_atlas_points_to_labeltable adjunct_aw_tableize_roi_info.py adjunct_calc_mont_dims.py
adjunct_combine_str.py adjunct_deob_around_origin adjunct_is_label.py adjunct_make_script_and_rst.py
adjunct_middle_pair_mask 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 afni_history afni_open
afni_proc.py afni_python_wrapper.py afni_skeleton.py afni_system_check.py
afni_vcheck aiv align_epi_anat.py ap_run_simple_rest.tcsh
ap_run_simple_rest_me.tcsh apqc_make_html.py apqc_make_tcsh.py apsearch
auto_warp.py balloon bayes_view build_afni.py
byteorder cat_matvec ccalc cdf
cifti_tool cjpeg colorbar_tool.py column_cat
compute_ROI_stats.tcsh convert_cdiflist_to_grads.py count count_afni
dcm2niix_afni desphinxify dicom_hdr dicom_hinfo
dicom_to_raw djpeg dsetstat2p eg_main_chrono.py
epi_b0_correct.py 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 fdrval
file_tool find_variance_lines.tcsh float_scan from3d a
gen_cluster_table 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 gtkyd_check gtkyd_check.py 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 lesion_align
make_pq_script.py make_random_timing.py make_stim_times.py map_TrackID
map_ap_to_deriv.py meica.py mycat neuro_deconvolve.py
nifti1_tool nifti_tool niml_feedme niprobe
nsize a open_apqc.py p2dsetstat parse_fs_lt_log.py
physio_calc.py plugout_drive plugout_ijk plugout_tt
prompt_popup prompt_user python_module_test.py quick.alpha.vals.py
quickspec quickspecSL quotize rPkgsInstall
read_matlab_files.py realtime_receiver.py roi_stats_warnings.py rotcom
rtfeedme serial_helper slow_surf_clustsim.py sswarper2
stimband strblast a suma suma_change_spec
tedana_wrapper.py test_afni_prog_help.tcsh timing_tool.py to3d
tokens uber_align_test.py uber_skel.py uber_subject.py
uber_ttest.py unWarpEPI.py uniq_images waver a
whereami whereami_afni whirlgif xmat_tool.py
README.3dsvm.realtime README.Ifile README.afnigui README.atlas_building
README.attributes README.bzip2 README.changes README.compression
README.copyright README.driver README.environment README.func_types
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 Feb 7 07:57:05 PM EST 2025 — RWCox