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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*

**** Documentation Page from Gang Chen ****

Links in the Table Below are to Individual -help Files
1dAstrip 1dBandpass 1dcat 1ddot
1deval 1dfft 1dFlagMotion 1dgenARMA11
1dgrayplot 1dMarry 1dmatcalc 1dnorm
1dplot 1dSEM 1dsum 1dsvd
1d_tool.py 1dtranspose 1dTsort 1dUpsample
24swap 2dImReg 2swap 3dABoverlap
3dAcost 3dAFNIto3D 3dAFNItoANALYZE 3dAFNItoMINC
3dAFNItoNIFTI 3dAFNItoNIML 3dAFNItoRaw 3dAllineate
3dANALYZEtoAFNI 3dAnatNudge 3dAnhist 3danisosmooth
3dANOVA 3dANOVA2 3dANOVA3 3dAttribute
3dAutobox 3dAutomask 3dAutoTcorrelate 3daxialize
3dBlurInMask 3dBlurToFWHM 3dBRAIN_VOYAGERtoAFNI 3dBrickStat
3dbuc2fim 3dbucket 3dcalc 3dClipLevel
3dclust 3dCM 3dConvolve 3dcopy
3dCRUISEtoAFNI 3dDeconvolve 3dDeconvolve_f 3ddelay
3dDespike 3dDetrend 3dDFT 3ddot
3dDTeig 3ddup 3dDWItoDT 3dedge3
3dEmpty 3dEntropy 3dErrtsCormat 3dExtrema
3dFDR 3dFFT 3dfim 3dfim+
3dFourier 3dfractionize 3dFriedman 3dFWHM
3dFWHMx 3dGetrow 3dhistog 3dinfo
3dIntracranial 3dInvFMRI 3dKruskalWallis 3dLocalBistat
3dLocalCormat 3dLocalstat 3dLocalSVD 3dLRflip
3dMannWhitney 3dmaskave 3dmaskdump 3dmaskSVD
3dmatcalc 3dmatmult 3dmaxima 3dMean
3dMedianFilter 3dmerge 3dMINCtoAFNI 3dnewid
3dNLfim 3dnoise 3dNotes 3dnvals
3dOverlap 3dPAR2AFNI.pl 3dpc 3dPeriodogram
3dproject 3dRank 3drefit 3dRegAna
3dREMLfit 3drename 3dresample 3dretroicor
3dROIstats 3drotate 3dRowFillin 3dSkullStrip
3dStatClust 3dSurf2Vol 3dSurfMask 3dSurfMaskDump
3dsvm 3dSynthesize 3dTagalign 3dTcat
3dTcorrelate 3dTcorrMap 3dTfitter 3dThreetoRGB
3dToutcount 3dTqual 3dTSgen 3dTshift
3dTsmooth 3dTsort 3dTstat 3dttest
3dTwotoComplex 3dUndump 3dUniformize 3dUpsample
3dVol2Surf 3dvolreg 3dWarp 3dWarpDrive
3dWavelets 3dWilcoxon 3dWinsor 3dZcat
3dZcutup 3dZeropad 3dZregrid @4Daverage
4swap abut @AddEdge adwarp
afni AFNI.afnirc AFNI_Batch_R afni_history
@AfniOrient2RAImap afni_proc.py afni_vcheck aiv
@Align_Centers align_epi_anat.py @align_partial_oblique AlphaSim
AnalyzeTrace @auto_align @auto_tlrc @build_afni_Xlib
byteorder cat_matvec ccalc cdf
@Center_Distance @CheckForAfniDset cjpeg @clip_volume
@CommandGlobb CompareSurfaces ConvertDset ConvertSurface
ConvexHull count CreateIcosahedron dicom_hdr
dicom_to_raw Dimon djpeg @DO.examples
@DoPerRoi.py DriveSuma DTIStudioFibertoSegments @DTI_studio_reposition
eg_main_chrono.py ent16 @fast_roi fdrval
file_tool @fix_FSsphere @float_fix float_scan
from3d @FromRAI FSread_annot @FS_roi_label
ftosh ge_header gen_epi_review.py @GetAfniBin
@GetAfniDims @GetAfniID @GetAfniOrient @GetAfniPrefix
@GetAfniRes @GetAfniView gifti_tool gui_xmat.py
Ifile im2niml imand imaver
imcalc imcat imcutup imdump
immask Imon imreg imrotate
imstack imstat imupsam inspec
@isOblique @IsoMasks IsoSurface lib_matplot.py
lib_realtime.py lib_RR_plot.py lpc_align.py MakeColorMap
@make_plug_diff make_random_timing.py @make_stim_file make_stim_times.py
MapIcosahedron mayo_analyze module_test_lib.py mpegtoppm
mritopgm neuro_deconvolve.py nifti1_test nifti_stats
nifti_tool niml_feedme @NoExt @NoisySkullStrip
@NoPound @np nsize option_list.py
@parse_afni_name @parse_name plugout_drive plugout_ijk
plugout_tt prompt_user @Purify_1D python_module_test.py
quickspec realtime_receiver.py @RenamePanga @Reorder
rmz ROI2dataset @ROI_Corr_Mat ROIgrow
rotcom RSFgen rtfeedme SampBias
ScaleToMap @ScaleVolume @ScriptCheck serial_helper
@ShowDynamicRange siemens_vision SpharmDeco @Spharm.examples
SpharmReco sqwave @statauxcode strblast
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
SurfInfo SurfMeasures SurfMesh SurfPatch
SurfQual SurfSmooth @SurfSmooth.HEAT_07.examples SurfToSurf
timing_tool.py to3d @ToRAI @TTxform_anat
@UpdateAfni @update.afni.binaries Vecwarp @VolCenter
waver whereami whirlgif xmat_tool.py
Xphace
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 Tue Nov 24 05:01:15 EST 2009 — RWCox

Created by Robert Cox
Last modified 2009-11-24 05:01
latest compile date
25 Nov 2009 04:20 EST
latest afni version
AFNI_2008_07_18_1710
 
 
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