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 1dplot.py
1dRplot 1dSEM 1dsound 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 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
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 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 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_lib.py
abids_tool.py abut a @AddEdge adwarp
afni @AfniEnv afni_history afni_open
@AfniOrient2RAImap afni_proc.py @afni_refacer_make_master @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_util.py afni_vcheck
aiv @Align_Centers align_epi_anat.py @align_partial_oblique
AlphaSim a AnalyzeTrace @ANATICOR 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
@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 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_calc_mont_dims.py @djunct_combine_str.py @djunct_dwi_selector.tcsh
@djunct_edgy_align_check @djunct_montage_coordinator @djunct_select_str.py @djunct_slice_space
@djunct_vol_3slice_select @DO.examples @DoPerRoi.py DriveSuma
DTIStudioFibertoSegments @DTI_studio_reposition eg_main_chrono.py @ElectroGrid
ent16 a @ExamineGenFeatDists ExamineXmat @extract_meica_ortvec
@fast_roi FATCAT_matplot 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 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_InstaCorr_Demo @Install_MEICA_Demo
@Install_NIH_Marmoset @Install_RSFMRI_Motion_Group_Demo @Install_TSrestMovieDemo InstaTract
@isOblique @IsoMasks IsoSurface lib_textdata.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 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 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 @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 Tue Feb 19 20:54:02 EST 2019 — RWCox