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
3dBrainSync 3dBRAIN_VOYAGERtoAFNI 3dBrickStat 3dbuc2fim a
3dbucket 3dcalc 3dClipLevel a 3dclust
3dClustCount 3dClusterize 3dClustSim 3dClustSimX
3dCM 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 3dExtractGroupInCorr 3dExtrema
3dFDR 3dFFT 3dfim 3dfim+
3dFourier 3dfractionize 3dFriedman 3dFWHM a
3dFWHMx 3dGenFeatureDist 3dGenPriors 3dGetrow
3dGrayplot 3dGroupInCorr 3dHist 3dhistog
3dinfill 3dinfo 3dIntracranial a 3dIntraVolMot
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
@3dMVM_validator 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
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 3dVec_to_RGBind 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_lib.py abids_tool.py abut a @AddEdge
adwarp afni @AfniEnv afnigui.html
afni_history afni_open @AfniOrient2RAImap afni_proc.py
afni_restproc.py @afni_R_package_install @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 @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 @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 ConvertDset ConvertSurface ConvexHull
count CreateIcosahedron dcm2niix_afni @DeblankFileNames
demo.fixed.niml.do demo.mobile.niml.do @DiceMetric dicom_hdr
dicom_hinfo dicom_to_raw @diff.files @diff.tree
Dimon Dimon1 djpeg @djunct_4d_imager
@djunct_calc_mont_dims.py @djunct_combine_str.py @djunct_dwi_imager @djunct_dwi_selector.bash
@djunct_select_str.py @DO.examples @DoPerRoi.py DriveSuma
DTIStudioFibertoSegments @DTI_studio_reposition eg_main_chrono.py @ElectroGrid
ent16 a @ExamineGenFeatDists ExamineXmat @extract_meica_ortvec
@fast_roi @FATCAT_heatmap_shiny FATCAT_matplot @FATCAT_matplot_shiny
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 @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 @grayplot 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_FATCAT_DEMO2 @Install_FATMVM_DEMO @Install_InstaCorr_Demo
@Install_MEICA_Demo @Install_NIH_Marmoset @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 @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 read_matlab_files.py realtime_receiver.py
@RenamePanga a @Reorder @RetinoProc RetroTS.py
@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 @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 @T1mask
@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
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 Wed May 23 20:29:46 EDT 2018 — RWCox