Program Help

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 3dmask_tool 3dmatcalc
3dmatmult 3dmaxima 3dMean
3dMedianFilter 3dMEMA 3dmerge
3dMINCtoAFNI a 3dnewid 3dNLfim
3dnoise a 3dNormalityTest 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 3dTnorm 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_restproc.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
@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 lib_textdata.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
@NoisySkullStrip nsize a @parse_afni_name
@NoisySkullStrip @parse_name ParseName
@NoisySkullStrip plugout_drive plugout_ijk
@NoisySkullStrip plugout_tt prompt_user
@NoisySkullStrip @Purify_1D python_module_test.py
@NoisySkullStrip quick.alpha.vals.py quickspec
@NoisySkullStrip @Quiet_Talkers @radial_correlate
@NoisySkullStrip realtime_receiver.py @RenamePanga a
@NoisySkullStrip @Reorder @RetinoProc
@NoisySkullStrip @R_funclist ROI2dataset
@NoisySkullStrip @ROI_Corr_Mat ROIgrow
@NoisySkullStrip rotcom RSFgen
@NoisySkullStrip rtfeedme SampBias
@NoisySkullStrip ScaleToMap @ScaleVolume
@NoisySkullStrip @ScriptCheck serial_helper
@NoisySkullStrip @Shift_Volume @ShowDynamicRange
@NoisySkullStrip siemens_vision a slow_surf_clustsim.py
@NoisySkullStrip SpharmDeco @Spharm.examples
@NoisySkullStrip SpharmReco sqwave a
@NoisySkullStrip strblast a suma
@NoisySkullStrip @SUMA_AlignToExperiment suma_change_spec
@NoisySkullStrip @SUMA_FSvolToBRIK @SUMA_Make_Spec_Caret
@NoisySkullStrip @SUMA_Make_Spec_FS @SUMA_Make_Spec_SF
@NoisySkullStrip Surf2VolCoord SurfaceMetrics
@NoisySkullStrip SurfClust SurfDist
@NoisySkullStrip SurfDsetInfo SurfExtrema
@NoisySkullStrip SurfFWHM SurfInfo
@NoisySkullStrip SurfMeasures SurfMesh
@NoisySkullStrip SurfPatch SurfQual
@NoisySkullStrip SurfRetinoMap SurfSmooth
@NoisySkullStrip @SurfSmooth.HEAT_07.examples SurfToSurf
@NoisySkullStrip @TimeDiff timing_tool.py
@NoisySkullStrip to3d @ToRAI
@NoisySkullStrip @TTxform_anat uber_align_test.py
@NoisySkullStrip uber_proc.py uber_skel.py
@NoisySkullStrip uber_subject.py uber_ttest.py
@NoisySkullStrip @update.afni.binaries Vecwarp
@NoisySkullStrip @VolCenter waver a
@NoisySkullStrip whereami whirlgif
@NoisySkullStrip xmat_tool.py Xphace a
@NoisySkullStrip README.3dsvm.realtime README.afnigui
@NoisySkullStrip README.atlas_building README.attributes
@NoisySkullStrip README.bzip2 README.changes
@NoisySkullStrip README.compression README.copyright
@NoisySkullStrip README.driver README.environment
@NoisySkullStrip README.func_types README.Ifile
@NoisySkullStrip README.notes README.permtest
@NoisySkullStrip README.plugouts README.realtime
@NoisySkullStrip README.registration README.render_scripts
@NoisySkullStrip README.roi README.setup
@NoisySkullStrip README.volreg README.web
@NoisySkullStrip README.ziad AFNI.changes.dglen
@NoisySkullStrip AFNI.changes.rickr AFNI.afnirc
@NoisySkullStrip AFNI.Xdefaults

This page auto-generated on Thu May 3 04:29:13 EDT 2012 — RWCox