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 1dplot.py
1dsound 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 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
@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 @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.tcsh @djunct_edgy_align_check
@djunct_montage_coordinator @djunct_select_str.py @djunct_slice_space @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 @xyz_to_ijk 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_json_tool.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
apqc_make_html.py apqc_make_tcsh.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 Tue Dec 11 18:14:32 EST 2018 — RWCox