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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
1dBandpass 1dcat 1ddot 1deval
1dfft 1dFlagMotion 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 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
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
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 @NoExt
@NoisySkullStrip @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 @RenamePanga 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 Fri Jul 3 05:17:17 EDT 2009 — RWCox

Created by Robert Cox
Last modified 2009-07-03 05:17
latest compile date
03 Jul 2009 04:16 EDT
latest afni version
AFNI_2008_07_18_1710
 
 
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