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 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 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 3dRSFC 3dSeg
3dSetupGroupInCorr 3dSharpen 3dSignatures 3dSkullStrip
3dSliceNDice 3dSpaceTimeCorr 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_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 @AfniEnv
afni_history afni_open @AfniOrient2RAImap afni_proc.py
afni_python_wrapper.py @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 @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 @CheckForAfniDset cifti_tool cjpeg
@clean_help_dir @clip_volume @ClustExp_CatLab ClustExp_HistTable.py
@ClustExp_run_shiny ClustExp_StatParse.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_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 @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_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
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 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 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
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 Thu Oct 31 09:45:54 PM EDT 2024 — RWCox