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
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 3dExchange 3dExtractGroupInCorr
3dExtrema 3dFDR 3dFFT 3dFWHM a
3dFWHMx 3dFourier 3dFriedman 3dGenFeatureDist
3dGenPriors 3dGetrow 3dGrayplot 3dGroupInCorr
3dHist 3dICC 3dISC 3dIntracranial a
3dInvFMRI 3dKruskalWallis 3dLFCD 3dLME
3dLRflip 3dLSS 3dLocalACF 3dLocalBistat
3dLocalHistog 3dLocalPV 3dLocalSVD 3dLocalstat
3dLombScargle 3dMEMA 3dMEPFM 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 3dPVmap 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 @afni_refacer_make_master @afni_refacer_make_onebigA12
@afni_refacer_run @align_partial_oblique @animal_warper @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_glue_imgs_vert @djunct_is_label.py
@djunct_json_value.py @djunct_make_script_and_rst.py @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 MBA MakeColorMap MapIcosahedron
ParseName RBA 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_check_omp 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 demoExpt.py
dicom_hdr dicom_hinfo dicom_to_raw djpeg
dsetstat2p eg_main_chrono.py ent16 a epi_b0_correct.py
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_latest_tgz.csh 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 Aug 16 18:07:09 EDT 2019 — RWCox