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 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
3dMEPFM 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 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_lib.py abids_tool.py
abut a @AddEdge adwarp afni
afni_check_omp @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_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 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 Wed Apr 24 18:59:19 EDT 2019 — RWCox