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]
1dAstrip 1dBandpass 1dBport 1dCorrelate
1dDW_Grad_o_Mat 1dDW_Grad_o_Mat++ 1dFlagMotion 1dMarry
1dNLfit 1dRplot 1dSEM 1dTsort
1dUpsample 1d_tool.py 1dcat 1ddot
1deval 1dfft 1dgenARMA11 1dgrayplot
1dmatcalc 1dnorm 1dplot 1dsum
1dsvd 1dtranspose 24swap a 2dImReg
2perm 2swap a 3dABoverlap 3dAFNIto3D
3dAFNItoANALYZE a 3dAFNItoMINC a 3dAFNItoNIFTI 3dAFNItoNIML
3dAFNItoRaw 3dANALYZEtoAFNI 3dANOVA 3dANOVA2
3dANOVA3 3dAllineate 3dAmpToRSFC 3dAnatNudge a
3dAnhist a 3dAttribute 3dAutoTcorrelate 3dAutobox
3dAutomask 3dBRAIN_VOYAGERtoAFNI 3dBandpass 3dBlurInMask
3dBlurToFWHM 3dBrainSync 3dBrickStat 3dCM
3dCRUISEtoAFNI 3dClipLevel a 3dClustCount 3dClustSim
3dClusterize 3dConformist 3dConvolve 3dCountSpikes
3dDFT 3dDTeig 3dDTtoDWI 3dDTtoNoisyDWI
3dDWItoDT 3dDWUncert 3dDeconvolve 3dDeconvolve_f a
3dDegreeCentrality 3dDespike 3dDetrend 3dECM
3dEigsToDT 3dEmpty 3dEntropy 3dExtractGroupInCorr
3dExtrema 3dFDR 3dFFT 3dFWHM a
3dFWHMx 3dFourier 3dFriedman 3dGenFeatureDist
3dGenPriors 3dGetrow 3dGrayplot 3dGroupInCorr
3dHist 3dIntraVolMot 3dIntracranial a 3dInvFMRI
3dKruskalWallis 3dLFCD 3dLME 3dLRflip
3dLSS 3dLocalACF 3dLocalBistat 3dLocalHistog
3dLocalPV 3dLocalSVD 3dLocalstat 3dLombScargle
3dMEMA 3dMINCtoAFNI a 3dMSE 3dMVM
3dMVM_validator 3dMannWhitney 3dMaskToASCII 3dMatch
3dMean 3dMedianFilter 3dMultiThresh 3dNLfim
3dNetCorr 3dNormalityTest 3dNotes 3dNwarpAdjust
3dNwarpApply 3dNwarpCalc 3dNwarpCat 3dNwarpFuncs
3dNwarpXYZ 3dOverlap 3dPAR2AFNI.pl 3dPFM
3dPeriodogram 3dPolyfit 3dProbTrackID 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 3dUniformize 3dUpsample 3dVecRGB_to_HSL
3dVol2Surf 3dWarp a 3dWarpDrive a 3dWavelets a
3dWilcoxon 3dWinsor 3dXClustSim 3dXYZcat
3dZcat 3dZcutup 3dZeropad 3dZipperZapper
3dZregrid 3danisosmooth 3daxialize a 3dbuc2fim a
3dbucket 3dcalc 3dclust 3dcopy
3ddelay 3ddot a 3ddot_beta 3ddup a
3dedge3 3dfim 3dfim+ 3dfractionize
3dhistog 3dinfill 3dinfo 3dkmeans
3dmaskSVD 3dmask_tool 3dmaskave 3dmaskdump
3dmatcalc 3dmatmult 3dmaxima 3dmerge
3dnewid 3dnoise a 3dnvals 3dpc
3dproject a 3drefit 3drename 3dresample
3dretroicor 3drotate 3dsvm 3dsvm_linpredict
3dtoXdataset 3dttest 3dttest++ 3dvolreg
4swap a @1dDiffMag @2dwarper.Allin @3dMVM_validator
@4Daverage @ANATICOR @AddEdge @AfniEnv
@AfniOrient2RAImap @Align_Centers @Atlasize @Center_Distance
@CheckForAfniDset @ClustExp_CatLab @ClustExp_run_shiny @CommandGlobb
@DO.examples @DTI_studio_reposition @DeblankFileNames @DiceMetric
@DoPerRoi.py @ElectroGrid @ExamineGenFeatDists @FATCAT_heatmap_shiny
@FATCAT_matplot_shiny @FS_roi_label @FSlabel2dset @FromRAI
@FullPath @GetAfniBin @GetAfniDims @GetAfniID
@GetAfniOrient @GetAfniPrefix @GetAfniRes @GetAfniView
@GradFlipTest @Install_3dPFM_Demo @Install_AfniRetinoDemo @Install_ClustScat_Demo
@Install_D99_macaque @Install_DBSproc @Install_FATCAT_DEMO @Install_FATCAT_DEMO2
@Install_FATMVM_DEMO @Install_InstaCorr_Demo @Install_MEICA_Demo @Install_NIH_Marmoset
@Install_RSFMRI_Motion_Group_Demo @Install_TSrestMovieDemo @IsoMasks @MakeLabelTable
@NoExt @NoPound @NoisySkullStrip @Purify_1D
@Quiet_Talkers @ROI_Corr_Mat @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 @align_partial_oblique @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_calc_mont_dims.py @djunct_combine_str.py
@djunct_dwi_selector.bash @djunct_dwi_selector.tcsh @djunct_select_str.py @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 @make_stim_file
@measure_bb_thick @measure_erosion_thick @measure_in2out @move.to.series.dirs
@np @parse_afni_name @parse_name @radial_correlate
@simulate_motion @snapshot_volreg @snapshot_volreg3 @suma_reprefixize_spec
@surf_to_vol_spackle @thickness_master @toMNI_Awarp @toMNI_Qwarpar
@update.afni.binaries AlphaSim a AnalyzeTrace BayesianGroupAna.py
BrainSkin CA_EZ_atlas.csh ClustExp_HistTable.py ClustExp_StatParse.py
CompareSurfaces ConvertDset ConvertSurface ConvexHull
CreateIcosahedron DTIStudioFibertoSegments Dimon Dimon1
DriveSuma ExamineXmat FATCAT_matplot FIRdesign
FSread_annot GLTsymtest HalloSuma Ifile a
InstaTract IsoSurface MakeColorMap MapIcosahedron
ParseName ROI2dataset ROIgrow RSFgen
RetroTS.py SampBias ScaleToMap SpharmDeco
SpharmReco Surf2VolCoord SurfClust SurfDist
SurfDsetInfo SurfExtrema SurfFWHM SurfInfo
SurfMeasures SurfMesh SurfPatch SurfQual
SurfRetinoMap SurfSmooth SurfToSurf SurfaceMetrics
Vecwarp Xphace a abids_json_info.py abids_lib.py
abids_tool.py abut a adwarp afni
afni_history afni_open afni_proc.py afni_restproc.py
afni_skeleton.py afni_system_check.py afni_util.py afni_vcheck
aiv align_epi_anat.py apsearch auto_warp.py
balloon byteorder cat_matvec ccalc
cdf cifti_tool cjpeg column_cat
count dcm2niix_afni dicom_hdr dicom_hinfo
dicom_to_raw djpeg eg_main_chrono.py ent16 a
fat_lat_csv.py fat_mat_sel.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 fdrval
file_tool float_scan from3d a ftosh a
ge_header a 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 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
lib_textdata.py make_pq_script.py make_random_timing.py make_stim_times.py
map_TrackID mayo_analyze a meica.py mritopgm a
mycat neuro_deconvolve.py nifti1_test nifti1_tool
nifti_tool niml_feedme niprobe nsize a
p2dsetstat parse_fs_lt_log.py plugout_drive plugout_ijk
plugout_tt prompt_popup prompt_user python_module_test.py
quick.alpha.vals.py quickspec quotize rPkgsInstall
read_matlab_files.py realtime_receiver.py rotcom rtfeedme
serial_helper siemens_vision a slow_surf_clustsim.py sqwave a
stimband strblast a suma suma_change_spec
tedana_wrapper.py 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
whirlgif xmat_tool.py
README.3dsvm.realtime README.Ifile 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.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 Wed Aug 22 17:59:00 EDT 2018 — RWCox