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 1dcat
1dCorrelate @1dDiffMag 1ddot 1deval
1dfft 1dFlagMotion 1dgenARMA11 1dgrayplot
1dMarry 1dmatcalc 1dnorm 1dplot
1dRplot 1dSEM 1dsum 1dsvd
1d_tool.py 1dtranspose 1dTsort 1dUpsample
24swap a 2dImReg @2dwarper.Allin 2swap a
3dABoverlap 3dAFNIto3D 3dAFNItoANALYZE a 3dAFNItoMINC a
3dAFNItoNIFTI 3dAFNItoNIML 3dAFNItoRaw 3dAllineate
3dANALYZEtoAFNI 3dAnatNudge a 3dAnhist a 3danisosmooth
3dANOVA 3dANOVA2 3dANOVA3 3dAttribute
3dAutobox 3dAutomask 3dAutoTcorrelate 3daxialize a
3dBandpass 3dBlurInMask 3dBlurToFWHM 3dBRAIN_VOYAGERtoAFNI
3dBrickStat 3dbuc2fim a 3dbucket 3dcalc
3dClipLevel a 3dclust 3dClustSim 3dCM
3dConvolve 3dcopy 3dCountSpikes 3dCRUISEtoAFNI
3dDeconvolve 3dDeconvolve_f a 3ddelay 3dDespike
3dDetrend 3dDFT 3ddot a 3dDTeig
3dDTtoDWI 3ddup a 3dDWItoDT 3dedge3
3dEmpty 3dEntropy 3dExtrema 3dFDR
3dFFT 3dfim 3dfim+ 3dFourier
3dfractionize 3dFriedman 3dFWHM a 3dFWHMx
3dGenPriors 3dGetrow 3dGroupInCorr 3dhistog
3dinfill 3dinfo 3dIntracranial a 3dInvFMRI
3dkmeans 3dKruskalWallis 3dLocalBistat 3dLocalPV
3dLocalstat 3dLocalSVD 3dLRflip 3dLSS
3dMannWhitney 3dmaskave 3dmaskdump 3dmaskSVD
3dMaskToASCII 3dmatcalc 3dmatmult 3dmaxima
3dMean 3dMedianFilter 3dmerge 3dMINCtoAFNI a
3dnewid 3dNLfim 3dnoise a 3dNotes
3dnvals 3dNwarpApply 3dNwarpCalc 3dOverlap
3dPAR2AFNI.pl 3dpc 3dPeriodogram 3dPolyfit
3dproject a 3dRank 3drefit 3dRegAna
3dREMLfit 3drename 3dresample 3dRetinoPhase
3dretroicor 3dROIstats 3drotate 3dRowFillin
3dSeg 3dSetupGroupInCorr 3dSignatures 3dSkullStrip
3dStatClust 3dSurf2Vol 3dSurfMask 3dSurfMaskDump
3dsvm 3dSynthesize 3dTagalign 3dTcat
3dTcorr1D 3dTcorrelate 3dTcorrMap 3dTfitter
3dThreetoRGB 3dToutcount 3dTqual 3dTSgen
3dTshift 3dTsmooth 3dTsort 3dTstat
3dttest 3dttest++ 3dTwotoComplex 3dUndump
3dUniformize 3dUpsample 3dVol2Surf 3dvolreg
3dWarp a 3dWarpDrive a 3dWavelets a 3dWilcoxon
3dWinsor 3dXYZcat 3dZcat 3dZcutup
3dZeropad 3dZregrid @4Daverage 4swap a
abut a @AddEdge adwarp afni
AFNI.afnirc @AfniEnv afni_history @AfniOrient2RAImap
afni_proc.py afni_vcheck aiv @Align_Centers
align_epi_anat.py @align_partial_oblique AlphaSim a AnalyzeTrace
@ANATICOR apsearch @Atlasize @auto_tlrc
@build_afni_Xlib byteorder cat_matvec ccalc
cdf @Center_Distance @CheckForAfniDset cjpeg
@clean_help_dir @clip_volume @CommandGlobb CompareSurfaces
ConvertDset ConvertSurface ConvexHull count
CreateIcosahedron @DeblankFileNames @DiceMetric dicom_hdr
dicom_hinfo dicom_to_raw Dimon djpeg
@DO.examples @DoPerRoi.py DriveSuma DTIStudioFibertoSegments
@DTI_studio_reposition eg_main_chrono.py @ElectroGrid ent16 a
ExamineXmat @fast_roi fdrval file_tool
@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 @GetAfniBin @GetAfniDims
@GetAfniID @GetAfniOrient @GetAfniPrefix @GetAfniRes
@GetAfniView gifti_tool @global_parse gui_uber_align_test.py
gui_uber_skel.py gui_uber_subj.py @help.AFNI Ifile a
im2niml a imand a imaver a imcalc a
imcat a imcutup a imdump a immask a
Imon imreg a imrotate a imstack a
imstat a imupsam a inspec @Install_InstaCorr_Demo
@isOblique @IsoMasks IsoSurface lib_matplot.py
lib_qt_gui.py MakeColorMap @MakeLabelTable @make_plug_diff
make_pq_script.py make_random_timing.py @make_stim_file make_stim_times.py
MapIcosahedron mayo_analyze a mpegtoppm mritopgm a
mycat neuro_deconvolve.py nifti1_test nifti_stats
nifti_tool niml_feedme @NoExt @NoisySkullStrip
@NoPound @np nsize a @parse_afni_name
@parse_name ParseName plugout_drive plugout_ijk
plugout_tt prompt_user @Purify_1D python_module_test.py
quick.alpha.vals.py quickspec @Quiet_Talkers @radial_correlate
realtime_receiver.py @RenamePanga a @Reorder @RetinoProc
@R_funclist ROI2dataset @ROI_Corr_Mat ROIgrow
rotcom RSFgen rtfeedme SampBias
ScaleToMap @ScaleVolume @ScriptCheck serial_helper
@Shift_Volume @ShowDynamicRange siemens_vision a slow_surf_clustsim.py
SpharmDeco @Spharm.examples SpharmReco sqwave a
strblast a suma @SUMA_AlignToExperiment suma_change_spec
@SUMA_FSvolToBRIK @SUMA_Make_Spec_Caret @SUMA_Make_Spec_FS @SUMA_Make_Spec_SF
Surf2VolCoord SurfaceMetrics SurfClust SurfDist
SurfDsetInfo SurfExtrema SurfFWHM SurfInfo
SurfMeasures SurfMesh SurfPatch SurfQual
SurfRetinoMap SurfSmooth @SurfSmooth.HEAT_07.examples SurfToSurf
@TimeDiff timing_tool.py to3d @ToRAI
@TTxform_anat uber_align_test.py uber_proc.py uber_skel.py
uber_subject.py uber_ttest.py @update.afni.binaries Vecwarp
@VolCenter waver a whereami whirlgif
xmat_tool.py Xphace a
README.3dsvm.realtime README.afnigui README.atlas_building README.attributes
README.bzip2 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 Sat Feb 11 05:31:58 EST 2012 — RWCox