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 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_calc_mont_dims.py @djunct_combine_str.py
@djunct_dwi_imager @djunct_dwi_selector.bash @djunct_dwi_selector.tcsh @djunct_select_str.py
@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 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_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_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 Jul 6 16:52:47 EDT 2018 — RWCox