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AFNI program -help files

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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 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 Thu May 3 04:29:13 EDT 2012 — RWCox


Created by Robert Cox
Last modified 2012-05-03 04:29
 

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