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 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 3dClustSimX 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 3dIntraVolMot
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 3dVec_to_RGBind 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 @3dMVM_validator @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 @FATCAT_heatmap_shiny @FATCAT_matplot_shiny
@FS_roi_label @FSlabel2dset @FromRAI @FullPath
@GetAfniBin @GetAfniDims @GetAfniID @GetAfniOrient
@GetAfniPrefix @GetAfniRes @GetAfniView @GradFlipTest
@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 @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 @T1mask @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_imager @djunct_dwi_selector.bash
@djunct_dwi_selector.tcsh @djunct_select_str.py @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
@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 AFNI.sumarc 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 Imon 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
afni_xmat.py afnigui.html aiv align_epi_anat.py
apsearch auto_warp.py balloon byteorder
cat_matvec ccalc cdf cifti_tool
cjpeg column_cat count dcm2niix_afni
demo.fixed.niml.do demo.mobile.niml.do 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_matplot.py lib_textdata.py lib_uber_stuff.py lib_wx.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 Fri Sep 21 16:23:51 EDT 2018 — RWCox