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 1dcat
1dCorrelate @1dDiffMag 1ddot 1dDW_Grad_o_Mat
1dDW_Grad_o_Mat++ 1deval 1dfft 1dFlagMotion
1dgenARMA11 1dgrayplot 1dMarry 1dmatcalc
1dNLfit 1dnorm 1dplot 1dRplot
1dSEM 1dsum 1dsvd 1d_tool.py
1dtranspose 1dTsort 1dUpsample 24swap a
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 3dBandpass 3dBlurInMask 3dBlurToFWHM
3dBRAIN_VOYAGERtoAFNI 3dBrickStat 3dbuc2fim a 3dbucket
3dcalc 3dClipLevel a 3dclust 3dClustCount
3dClustSim 3dClustSimX 3dCM 3dConformist
3dConvolve 3dcopy 3dCountSpikes 3dCRUISEtoAFNI
3dDeconvolve 3dDeconvolve_f a 3dDegreeCentrality 3ddelay
3dDespike 3dDetrend 3dDFT 3ddot a
3ddot_beta 3dDTeig 3dDTtoDWI 3ddup a
3dDWItoDT 3dDWUncert 3dECM 3dedge3
3dEmpty 3dEntropy 3dExtractGroupInCorr 3dExtrema
3dFDR 3dFFT 3dfim 3dfim+
3dFourier 3dfractionize 3dFriedman 3dFWHM a
3dFWHMx 3dGenFeatureDist 3dGenPriors 3dGetrow
3dGroupInCorr 3dHist 3dhistog 3dinfill
3dinfo 3dIntracranial a 3dInvFMRI 3dkmeans
3dKruskalWallis 3dLFCD 3dLME 3dLocalACF
3dLocalBistat 3dLocalHistog 3dLocalPV 3dLocalstat
3dLocalSVD 3dLombScargle 3dLRflip 3dLSS
3dMannWhitney 3dmaskave 3dmaskdump 3dmaskSVD
3dMaskToASCII 3dmask_tool 3dmatcalc 3dMatch
3dmatmult 3dmaxima 3dMean 3dMedianFilter
3dMEMA 3dmerge 3dMINCtoAFNI a 3dMSE
3dMultiThresh 3dMVM 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
3dQwarp 3dRank 3dRankizer 3drefit
3dRegAna 3dReHo 3dREMLfit 3drename
3dresample 3dRetinoPhase 3dretroicor 3dROIMaker
3dROIstats 3drotate 3dRowFillin 3dRprogDemo
3dRSFC 3dSeg 3dSetupGroupInCorr 3dSharpen
3dSignatures 3dSkullStrip 3dSpaceTimeCorr 3dStatClust
3dSurf2Vol 3dSurfMask 3dsvm 3dsvm_linpredict
3dSynthesize 3dTagalign 3dTcat 3dTcorr1D
3dTcorrelate 3dTcorrMap 3dTfilter 3dTfitter
3dThreetoRGB 3dTnorm 3dToutcount 3dtoXdataset
3dToyProg 3dTproject 3dTqual 3dTrackID
3dTRfix 3dTSgen 3dTshift 3dTsmooth
3dTsort 3dTsplit4D 3dTstat 3dttest
3dttest++ 3dTwotoComplex 3dUndump 3dUnifize
3dUniformize 3dUpsample 3dVecRGB_to_HSL 3dVec_to_RGBind
3dVol2Surf 3dvolreg 3dWarp a 3dWarpDrive a
3dWavelets a 3dWilcoxon 3dWinsor 3dXClustSim
3dXYZcat 3dZcat 3dZcutup 3dZeropad
3dZregrid @4Daverage 4swap a abut a
@AddEdge adwarp afni AFNI_atlas_spaces.niml
@AfniEnv afnigui.html afni_history afni_open
@AfniOrient2RAImap afni_proc.py afni_restproc.py @afni.run.me
afni_skeleton.py AFNI.sumarc afni_system_check.py afni_util.py
afni_vcheck afni_xmat.py aiv @Align_Centers
align_epi_anat.py @align_partial_oblique AlphaSim a AnalyzeTrace
@ANATICOR apsearch ask_me.py @Atlasize
@auto_tlrc auto_warp.py balloon BrainSkin
@build_afni_Xlib byteorder CA_EZ_atlas.csh cat_matvec
ccalc cdf @Center_Distance @chauffeur_afni
@CheckForAfniDset cifti_tool cjpeg @clean_help_dir
@clip_volume column_cat @CommandGlobb CompareSurfaces
@compute_gcor ConvertDset ConvertSurface ConvexHull
count CreateIcosahedron @DeblankFileNames demo.fixed.niml.do
demo.mobile.niml.do @DiceMetric dicom_hdr dicom_hinfo
dicom_to_raw @diff.files @diff.tree Dimon
Dimon1 Dimon.xorg7_64 djpeg @djunct_calc_mont_dims.py
@djunct_dwi_imager @DO.examples @DoPerRoi.py DriveSuma
DTIStudioFibertoSegments @DTI_studio_reposition eg_main_chrono.py @ElectroGrid
ent16 a @ExamineGenFeatDists ExamineXmat @fast_roi
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_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 @GetAfniOrient @GetAfniPrefix @GetAfniRes
@get.afni.version @GetAfniView gifti_tool @global_parse
GLTsymtest @GradFlipTest HalloSuma @help.AFNI
Ifile a im2niml a images_equal imand a
imaver a imcalc a imcat a imcutup a
imdump a immask a Imon imreg a
imrotate a imstack a imstat a imupsam a
inspec @Install_3dPFM_Demo @Install_AfniRetinoDemo @Install_Cambridge_Demo
@Install_ClustScat_Demo @Install_D99_macaque @Install_DBSproc @Install_FATCAT_DEMO
@Install_FATMVM_DEMO @Install_InstaCorr_Demo @Install_MEICA_Demo @Install_PTaylor_TractDemo
@Install_RSFMRI_Motion_Group_Demo @Install_TSrestMovieDemo InstaTract @isOblique
@IsoMasks IsoSurface lib_matplot.py lib_textdata.py
lib_uber_stuff.py lib_wx.py MakeColorMap @MakeLabelTable
@make_plug_diff make_pq_script.py make_random_timing.py @make_stim_file
make_stim_times.py MapIcosahedron map_TrackID mayo_analyze a
meica.py @move.to.series.dirs mpegtoppm mritopgm a
mycat neuro_deconvolve.py nifti1_test nifti1_tool
nifti_tool niml_feedme niprobe @NoExt
@NoisySkullStrip @NoPound @np nsize a
@parse_afni_name parse_fs_lt_log.py @parse_name ParseName
plugout_drive plugout_ijk plugout_tt prompt_user
@Purify_1D python_module_test.py quick.alpha.vals.py quickspec
@Quiet_Talkers quotize @radial_correlate read_matlab_files.py
realtime_receiver.py @RenamePanga a @Reorder @RetinoProc
@R_funclist ROI2dataset @ROI_Corr_Mat ROIgrow
rotcom rPkgsInstall RSFgen rtfeedme
SampBias ScaleToMap @ScaleVolume @ScriptCheck
serial_helper @Shift_Volume @ShowDynamicRange siemens_vision a
@simulate_motion @simulate.motion 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
Surf2VolCoord SurfaceMetrics SurfClust SurfDist
SurfDsetInfo SurfExtrema SurfFWHM SurfInfo
SurfMeasures SurfMesh SurfPatch SurfQual
SurfRetinoMap SurfSmooth @SurfSmooth.HEAT_07.examples SurfToSurf
@T1mask @T1scale @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
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 Fri Mar 10 22:51:45 EST 2017 — RWCox