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 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 3dAFNItoMINC a
3dAFNItoNIFTI 3dAFNItoNIML 3dAFNItoRaw 3dAllineate
3dAmpToRSFC 3dANALYZEtoAFNI 3dAnatNudge a 3dAnhist a
3danisosmooth 3dANOVA 3dANOVA2 3dANOVA3
3dAttribute 3dAutobox 3dAutomask 3dAutoTcorrelate
3daxialize a 3dBallMatch 3dBandpass 3dBlurInMask
3dBlurToFWHM 3dBrainSync 3dBRAIN_VOYAGERtoAFNI 3dBrickStat
3dbuc2fim a 3dbucket 3dcalc 3dClipLevel a
3dclust 3dClustCount 3dClusterize 3dClustSim
3dCM 3dCompareAffine 3dConformist 3dConvolve
3dcopy 3dCountSpikes 3dCRUISEtoAFNI 3dDeconvolve
3dDeconvolve_f a 3dDegreeCentrality 3ddelay 3dDespike
3dDetrend 3dDFT 3ddot a 3ddot_beta
3dDTeig 3dDTtoDWI 3dDTtoNoisyDWI 3ddup a
3dDWItoDT 3dDWUncert 3dECM 3dedge3
3dEigsToDT 3dEmpty 3dEntropy 3dExchange
3dExtractGroupInCorr 3dExtrema 3dFDR 3dFFT
3dfim 3dfim+ 3dFourier 3dfractionize
3dFriedman 3dFWHM a 3dFWHMx 3dGenFeatureDist
3dGenPriors 3dGetrow 3dGrayplot 3dGroupInCorr
3dHist 3dhistog 3dICC 3dinfill
3dinfo 3dIntracranial a 3dInvFMRI 3dISC
3dkmeans 3dKruskalWallis 3dLFCD 3dLME
3dLMEr 3dLocalACF 3dLocalBistat 3dLocalHistog
3dLocalPV 3dLocalstat 3dLocalSVD 3dLombScargle
3dLRflip 3dLSS 3dMannWhitney 3dmaskave
3dmaskdump 3dmaskSVD 3dMaskToASCII 3dmask_tool
3dmatcalc 3dMatch 3dmatmult 3dmaxima
3dMean 3dMedianFilter 3dMEMA 3dMEPFM
3dmerge 3dMINCtoAFNI a 3dMSE 3dMSS
3dMultiThresh 3dMVM 3dMVM_validator 3dNetCorr
3dnewid 3dNLfim 3dnoise a 3dNormalityTest
3dNotes 3dnvals 3dNwarpAdjust 3dNwarpApply
3dNwarpCalc 3dNwarpCat 3dNwarpFuncs 3dNwarpXYZ
3dOverlap 3dPAR2AFNI.pl 3dpc 3dPeriodogram
3dPFM 3dPolyfit 3dProbTrackID 3dproject a
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
3dttest++ 3dTto1D 3dTwotoComplex 3dUndump
3dUnifize 3dUniformize 3dUpsample 3dVecRGB_to_HSL
3dVol2Surf 3dvolreg 3dWarp a 3dWarpDrive a
3dWavelets a 3dWilcoxon 3dWinsor 3dXClustSim
3dXYZcat 3dZcat 3dZcutup 3dZeropad
3dZipperZapper 3dZregrid @4Daverage 4swap a
abids_json_info.py abids_json_tool.py abids_tool.py abut a
@AddEdge adjunct_aw_tableize_roi_info.py adjunct_calc_mont_dims.py adjunct_combine_str.py
adjunct_is_label.py adjunct_make_script_and_rst.py adjunct_select_str.py adjunct_simplify_cost.py
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_restproc.py
@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 AlphaSim a AnalyzeTrace @ANATICOR
@animal_warper apqc_make_html.py apqc_make_tcsh.py apsearch
@Atlasize @auto_tlrc auto_warp.py balloon
BayesianGroupAna.py BrainSkin @build_afni_Xlib byteorder
CA_EZ_atlas.csh cat_matvec ccalc cdf
@Center_Distance @chauffeur_afni check_dset_for_fs.py @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 convert_cdiflist_to_grads.py ConvertDset ConvertSurface
ConvexHull count CreateIcosahedron dcm2niix_afni
@DeblankFileNames demoExpt.py @DiceMetric dicom_hdr
dicom_hinfo dicom_to_raw @diff.files @diff.tree
Dimon Dimon1 djpeg @djunct_4d_imager
@djunct_4d_slices_to_3d_vol @djunct_anonymize @djunct_calc_mont_dims.py @djunct_combine_str.py
@djunct_dwi_selector.tcsh @djunct_edgy_align_check @djunct_glue_imgs_vert @djunct_is_label.py
@djunct_json_value.py @djunct_make_script_and_rst.py @djunct_modal_smoothing_with_rep @djunct_montage_coordinator
@djunct_overlap_check @djunct_select_str.py @djunct_slice_space @djunct_ssw_intermed_edge_imgs
@djunct_vol_3slice_select @DO.examples @DoPerRoi.py DoPerRoi.py
DriveSuma dsetstat2p DTIStudioFibertoSegments @DTI_studio_reposition
eg_main_chrono.py @ElectroGrid ent16 a epi_b0_correct.py
@ExamineGenFeatDists ExamineXmat @extract_meica_ortvec @fast_roi
FATCAT_matplot fat_lat_csv.py fat_mat2d_plot.py fat_mat_sel.py
fat_mat_tableize.py fat_mvm_gridconv.py fat_mvm_prep.py fat_mvm_review.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_grad_plot fat_proc_imit2w_from_t1w fat_proc_map_to_dti
fat_proc_select_vols fat_roi_row.py @fat_tract_colorize fdrval
file_tool FIRdesign @fix_FSsphere @float_fix
float_scan from3d a @FromRAI @FSlabel2dset
FSread_annot @FS_roi_label ftosh a @FullPath
ge_header a 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 HalloSuma @help.AFNI Ifile a
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 inspec @Install_3dPFM_Demo
@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_MEICA_Demo
@Install_NIH_Marmoset @Install_NMT @Install_RSFMRI_Motion_Group_Demo @Install_TSrestMovieDemo
InstaTract @isOblique @IsoMasks IsoSurface
MakeColorMap @MakeLabelTable make_latest_tgz.csh @make_plug_diff
make_pq_script.py make_random_timing.py @make_stim_file make_stim_times.py
MapIcosahedron map_TrackID mayo_analyze a MBA
@measure_bb_thick @measure_erosion_thick @measure_in2out meica.py
@move.to.series.dirs mritopgm a mycat neuro_deconvolve.py
nifti1_test nifti1_tool nifti_tool niml_feedme
niprobe @NoExt @NoisySkullStrip @NoPound
@np nsize a p2dsetstat @parse_afni_name
parse_fs_lt_log.py @parse_name ParseName plugout_drive
plugout_ijk plugout_tt prompt_popup prompt_user
@Purify_1D python_module_test.py quick.alpha.vals.py quickspec
@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
rotcom rPkgsInstall RSFgen rtfeedme
SampBias ScaleToMap @ScaleVolume @ScriptCheck
serial_helper @Shift_Volume @ShowDynamicRange siemens_vision a
@simulate_motion @SkullStrip_TouchUp slow_surf_clustsim.py @snapshot_volreg
@snapshot_volreg3 SpharmDeco @Spharm.examples SpharmReco
sqwave a @SSwarper stimband strblast a
suma @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 SurfMeasures SurfMesh SurfPatch
SurfQual SurfRetinoMap SurfSmooth @SurfSmooth.HEAT_07.examples
SurfToSurf @surf_to_vol_spackle @T1scale tedana_wrapper.py
@thickness_master @TimeDiff timing_tool.py to3d
tokens @toMNI_Awarp @toMNI_Qwarpar @ToRAI
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 whirlgif
xmat_tool.py Xphace a @xyz_to_ijk
README.3dsvm.realtime README.afnigui README.atlas_building README.attributes
README.bzip2 README.caez_atlas_build 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.volreg README.web README.ziad
AFNI.changes.dglen AFNI.changes.rickr AFNI.afnirc AFNI.Xdefaults

This page auto-generated on Thu Nov 12 20:22:57 EST 2020 — RWCox