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 2dcat
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
3dCompareAffine 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 3dExchange 3dExtractGroupInCorr
3dExtrema 3dFDR 3dFFT 3dfim
3dfim+ 3dFourier 3dfractionize 3dFriedman
3dFWHM a 3dFWHMx 3dGenFeatureDist 3dGenPriors
3dGetrow 3dGrayplot 3dGroupInCorr 3dHist
3dhistog 3dICC 3dinfill 3dinfo
3dIntracranial a 3dInvFMRI 3dISC 3dkmeans
3dKruskalWallis 3dLFCD 3dLME 3dLMEr
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_tool.py abut a @AddEdge adjunct_aw_tableize_roi_info.py
adjunct_calc_mont_dims.py adjunct_combine_str.py adjunct_is_label.py adjunct_make_script_and_rst.py
adjunct_select_str.py adjunct_simplify_cost.py adwarp afni
afni_check_omp @AfniEnv afni_history afni_open
@AfniOrient2RAImap afni_proc.py afni_python_wrapper.py @afni_refacer_make_master
@afni_refacer_make_master_addendum @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_vcheck aiv @Align_Centers align_epi_anat.py
@align_partial_oblique AlphaSim a AnalyzeTrace @ANATICOR
@animal_warper 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 check_dset_for_fs.py @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 convert_cdiflist_to_grads.py 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_anonymize @djunct_calc_mont_dims.py @djunct_combine_str.py
@djunct_dwi_selector.tcsh @djunct_edgy_align_check @djunct_glue_imgs_vert @djunct_is_label.py
@djunct_json_value.py @djunct_make_script_and_rst.py @djunct_modal_smoothing_with_rep @djunct_montage_coordinator
@djunct_select_str.py @djunct_slice_space @djunct_ssw_intermed_edge_imgs @djunct_vol_3slice_select
@DO.examples @DoPerRoi.py DoPerRoi.py DriveSuma
dsetstat2p DTIStudioFibertoSegments @DTI_studio_reposition eg_main_chrono.py
@ElectroGrid ent16 a epi_b0_correct.py @ExamineGenFeatDists
ExamineXmat @extract_meica_ortvec @fast_roi FATCAT_matplot
fat_lat_csv.py fat_mat2d_plot.py fat_mat_sel.py fat_mat_tableize.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_IBT_DATASETS @Install_InstaCorr_Demo
@Install_MACAQUE_DEMO @Install_MACAQUE_DEMO_REST @Install_MEICA_Demo @Install_NIH_Marmoset
@Install_NMT @Install_RSFMRI_Motion_Group_Demo @Install_TSrestMovieDemo InstaTract
@isOblique @IsoMasks IsoSurface 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 RBA read_matlab_files.py
realtime_receiver.py @RenamePanga a @Reorder @RetinoProc
RetroTS.py @R_funclist ROI2dataset @ROI_Corr_Mat
@ROI_decluster ROIgrow @ROI_modal_grow 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 Thu Sep 17 15:37:52 EDT 2020 — RWCox