:tocdepth: 2

.. _programs_main:

###################################
Alphabetical list of program helps
###################################

.. contents:: :local:

Links to program help files
----------------------------

This is a list of all AFNI programs.  Click on any name to see the
help for that program.

For additional reference, please also see the "classified" list of
helps :ref:`HERE<edu_class_prog>`\, where programs are loosely grouped
by topic and functionality, with a brief description of each provided.

.. csv-table::

   :ref:`1dApar2mat <ahelp_1dApar2mat>`,:ref:`1dAstrip <ahelp_1dAstrip>`,:ref:`1dBandpass <ahelp_1dBandpass>`
   :ref:`1dBport <ahelp_1dBport>`,:ref:`1dCorrelate <ahelp_1dCorrelate>`,:ref:`1dDW_Grad_o_Mat++ <ahelp_1dDW_Grad_o_Mat++>`
   :ref:`1dFlagMotion <ahelp_1dFlagMotion>`,:ref:`1dMarry <ahelp_1dMarry>`,:ref:`1dNLfit <ahelp_1dNLfit>`
   :ref:`1dRplot <ahelp_1dRplot>`,:ref:`1dSEM <ahelp_1dSEM>`,:ref:`1dTsort <ahelp_1dTsort>`
   :ref:`1dUpsample <ahelp_1dUpsample>`,:ref:`1d_tool.py <ahelp_1d_tool.py>`,:ref:`1dcat <ahelp_1dcat>`
   :ref:`1ddot <ahelp_1ddot>`,:ref:`1deval <ahelp_1deval>`,:ref:`1dfft <ahelp_1dfft>`
   :ref:`1dgenARMA11 <ahelp_1dgenARMA11>`,:ref:`1dgrayplot <ahelp_1dgrayplot>`,:ref:`1dmatcalc <ahelp_1dmatcalc>`
   :ref:`1dnorm <ahelp_1dnorm>`,:ref:`1dplot <ahelp_1dplot>`,:ref:`1dplot.py <ahelp_1dplot.py>`
   :ref:`1dsound <ahelp_1dsound>`,:ref:`1dsum <ahelp_1dsum>`,:ref:`1dsvd <ahelp_1dsvd>`
   :ref:`1dtranspose <ahelp_1dtranspose>`,:ref:`24swap <ahelp_24swap>`,:ref:`2dImReg <ahelp_2dImReg>`
   :ref:`2dcat <ahelp_2dcat>`,:ref:`2perm <ahelp_2perm>`,:ref:`2swap <ahelp_2swap>`
   :ref:`3dABoverlap <ahelp_3dABoverlap>`,:ref:`3dAFNIto3D <ahelp_3dAFNIto3D>`,:ref:`3dAFNItoANALYZE <ahelp_3dAFNItoANALYZE>`
   :ref:`3dAFNItoNIFTI <ahelp_3dAFNItoNIFTI>`,:ref:`3dAFNItoNIML <ahelp_3dAFNItoNIML>`,:ref:`3dAFNItoRaw <ahelp_3dAFNItoRaw>`
   :ref:`3dANOVA <ahelp_3dANOVA>`,:ref:`3dANOVA2 <ahelp_3dANOVA2>`,:ref:`3dANOVA3 <ahelp_3dANOVA3>`
   :ref:`3dAcost <ahelp_3dAcost>`,:ref:`3dAllineate <ahelp_3dAllineate>`,:ref:`3dAmpToRSFC <ahelp_3dAmpToRSFC>`
   :ref:`3dAnhist <ahelp_3dAnhist>`,:ref:`3dAttribute <ahelp_3dAttribute>`,:ref:`3dAutoTcorrelate <ahelp_3dAutoTcorrelate>`
   :ref:`3dAutobox <ahelp_3dAutobox>`,:ref:`3dAutomask <ahelp_3dAutomask>`,:ref:`3dBRAIN_VOYAGERtoAFNI <ahelp_3dBRAIN_VOYAGERtoAFNI>`
   :ref:`3dBallMatch <ahelp_3dBallMatch>`,:ref:`3dBandpass <ahelp_3dBandpass>`,:ref:`3dBlurInMask <ahelp_3dBlurInMask>`
   :ref:`3dBlurToFWHM <ahelp_3dBlurToFWHM>`,:ref:`3dBrainSync <ahelp_3dBrainSync>`,:ref:`3dBrickStat <ahelp_3dBrickStat>`
   :ref:`3dCM <ahelp_3dCM>`,:ref:`3dCRUISEtoAFNI <ahelp_3dCRUISEtoAFNI>`,:ref:`3dClipLevel <ahelp_3dClipLevel>`
   :ref:`3dClustCount <ahelp_3dClustCount>`,:ref:`3dClustSim <ahelp_3dClustSim>`,:ref:`3dClusterize <ahelp_3dClusterize>`
   :ref:`3dCompareAffine <ahelp_3dCompareAffine>`,:ref:`3dConformist <ahelp_3dConformist>`,:ref:`3dConvolve <ahelp_3dConvolve>`
   :ref:`3dDFT <ahelp_3dDFT>`,:ref:`3dDTeig <ahelp_3dDTeig>`,:ref:`3dDTtoDWI <ahelp_3dDTtoDWI>`
   :ref:`3dDTtoNoisyDWI <ahelp_3dDTtoNoisyDWI>`,:ref:`3dDWItoDT <ahelp_3dDWItoDT>`,:ref:`3dDWUncert <ahelp_3dDWUncert>`
   :ref:`3dDeconvolve <ahelp_3dDeconvolve>`,:ref:`3dDegreeCentrality <ahelp_3dDegreeCentrality>`,:ref:`3dDepthMap <ahelp_3dDepthMap>`
   :ref:`3dDespike <ahelp_3dDespike>`,:ref:`3dDetrend <ahelp_3dDetrend>`,:ref:`3dDiff <ahelp_3dDiff>`
   :ref:`3dECM <ahelp_3dECM>`,:ref:`3dEdu_01_scale <ahelp_3dEdu_01_scale>`,:ref:`3dEigsToDT <ahelp_3dEigsToDT>`
   :ref:`3dEmpty <ahelp_3dEmpty>`,:ref:`3dEntropy <ahelp_3dEntropy>`,:ref:`3dErrtsCormat <ahelp_3dErrtsCormat>`
   :ref:`3dExchange <ahelp_3dExchange>`,:ref:`3dExtractGroupInCorr <ahelp_3dExtractGroupInCorr>`,:ref:`3dExtrema <ahelp_3dExtrema>`
   :ref:`3dFDR <ahelp_3dFDR>`,:ref:`3dFFT <ahelp_3dFFT>`,:ref:`3dFWHMx <ahelp_3dFWHMx>`
   :ref:`3dFriedman <ahelp_3dFriedman>`,:ref:`3dGLMM <ahelp_3dGLMM>`,:ref:`3dGenFeatureDist <ahelp_3dGenFeatureDist>`
   :ref:`3dGenPriors <ahelp_3dGenPriors>`,:ref:`3dGetrow <ahelp_3dGetrow>`,:ref:`3dGrayplot <ahelp_3dGrayplot>`
   :ref:`3dGroupInCorr <ahelp_3dGroupInCorr>`,:ref:`3dHist <ahelp_3dHist>`,:ref:`3dICC <ahelp_3dICC>`
   :ref:`3dISC <ahelp_3dISC>`,:ref:`3dIntracranial <ahelp_3dIntracranial>`,:ref:`3dInvFMRI <ahelp_3dInvFMRI>`
   :ref:`3dKruskalWallis <ahelp_3dKruskalWallis>`,:ref:`3dLFCD <ahelp_3dLFCD>`,:ref:`3dLME <ahelp_3dLME>`
   :ref:`3dLME2 <ahelp_3dLME2>`,:ref:`3dLMEr <ahelp_3dLMEr>`,:ref:`3dLRflip <ahelp_3dLRflip>`
   :ref:`3dLSS <ahelp_3dLSS>`,:ref:`3dLocalACF <ahelp_3dLocalACF>`,:ref:`3dLocalBistat <ahelp_3dLocalBistat>`
   :ref:`3dLocalHistog <ahelp_3dLocalHistog>`,:ref:`3dLocalPV <ahelp_3dLocalPV>`,:ref:`3dLocalSVD <ahelp_3dLocalSVD>`
   :ref:`3dLocalUnifize <ahelp_3dLocalUnifize>`,:ref:`3dLocalstat <ahelp_3dLocalstat>`,:ref:`3dLombScargle <ahelp_3dLombScargle>`
   :ref:`3dMEMA <ahelp_3dMEMA>`,:ref:`3dMEPFM <ahelp_3dMEPFM>`,:ref:`3dMSE <ahelp_3dMSE>`
   :ref:`3dMSS <ahelp_3dMSS>`,:ref:`3dMVM <ahelp_3dMVM>`,:ref:`3dMVM_validator <ahelp_3dMVM_validator>`
   :ref:`3dMannWhitney <ahelp_3dMannWhitney>`,:ref:`3dMaskToASCII <ahelp_3dMaskToASCII>`,:ref:`3dMatch <ahelp_3dMatch>`
   :ref:`3dMean <ahelp_3dMean>`,:ref:`3dMedianFilter <ahelp_3dMedianFilter>`,:ref:`3dMultiThresh <ahelp_3dMultiThresh>`
   :ref:`3dNLfim <ahelp_3dNLfim>`,:ref:`3dNetCorr <ahelp_3dNetCorr>`,:ref:`3dNormalityTest <ahelp_3dNormalityTest>`
   :ref:`3dNotes <ahelp_3dNotes>`,:ref:`3dNwarpAdjust <ahelp_3dNwarpAdjust>`,:ref:`3dNwarpApply <ahelp_3dNwarpApply>`
   :ref:`3dNwarpCalc <ahelp_3dNwarpCalc>`,:ref:`3dNwarpCat <ahelp_3dNwarpCat>`,:ref:`3dNwarpFuncs <ahelp_3dNwarpFuncs>`
   :ref:`3dNwarpXYZ <ahelp_3dNwarpXYZ>`,:ref:`3dOverlap <ahelp_3dOverlap>`,:ref:`3dPAR2AFNI.pl <ahelp_3dPAR2AFNI.pl>`
   :ref:`3dPFM <ahelp_3dPFM>`,:ref:`3dPVmap <ahelp_3dPVmap>`,:ref:`3dPeriodogram <ahelp_3dPeriodogram>`
   :ref:`3dPolyfit <ahelp_3dPolyfit>`,:ref:`3dPval <ahelp_3dPval>`,:ref:`3dQwarp <ahelp_3dQwarp>`
   :ref:`3dREMLfit <ahelp_3dREMLfit>`,:ref:`3dROIMaker <ahelp_3dROIMaker>`,:ref:`3dROIstats <ahelp_3dROIstats>`
   :ref:`3dRSFC <ahelp_3dRSFC>`,:ref:`3dRank <ahelp_3dRank>`,:ref:`3dRankizer <ahelp_3dRankizer>`
   :ref:`3dReHo <ahelp_3dReHo>`,:ref:`3dRegAna <ahelp_3dRegAna>`,:ref:`3dRetinoPhase <ahelp_3dRetinoPhase>`
   :ref:`3dRowFillin <ahelp_3dRowFillin>`,:ref:`3dRprogDemo <ahelp_3dRprogDemo>`,:ref:`3dSeg <ahelp_3dSeg>`
   :ref:`3dSetupGroupInCorr <ahelp_3dSetupGroupInCorr>`,:ref:`3dSharpen <ahelp_3dSharpen>`,:ref:`3dSignatures <ahelp_3dSignatures>`
   :ref:`3dSkullStrip <ahelp_3dSkullStrip>`,:ref:`3dSliceNDice <ahelp_3dSliceNDice>`,:ref:`3dSpaceTimeCorr <ahelp_3dSpaceTimeCorr>`
   :ref:`3dSpatNorm <ahelp_3dSpatNorm>`,:ref:`3dStatClust <ahelp_3dStatClust>`,:ref:`3dSurf2Vol <ahelp_3dSurf2Vol>`
   :ref:`3dSurfMask <ahelp_3dSurfMask>`,:ref:`3dSynthesize <ahelp_3dSynthesize>`,:ref:`3dTORTOISEtoHere <ahelp_3dTORTOISEtoHere>`
   :ref:`3dTRfix <ahelp_3dTRfix>`,:ref:`3dTSgen <ahelp_3dTSgen>`,:ref:`3dTagalign <ahelp_3dTagalign>`
   :ref:`3dTcat <ahelp_3dTcat>`,:ref:`3dTcorr1D <ahelp_3dTcorr1D>`,:ref:`3dTcorrMap <ahelp_3dTcorrMap>`
   :ref:`3dTcorrelate <ahelp_3dTcorrelate>`,:ref:`3dTfilter <ahelp_3dTfilter>`,:ref:`3dTfitter <ahelp_3dTfitter>`
   :ref:`3dThreetoRGB <ahelp_3dThreetoRGB>`,:ref:`3dTnorm <ahelp_3dTnorm>`,:ref:`3dToutcount <ahelp_3dToutcount>`
   :ref:`3dToyProg <ahelp_3dToyProg>`,:ref:`3dTproject <ahelp_3dTproject>`,:ref:`3dTqual <ahelp_3dTqual>`
   :ref:`3dTrackID <ahelp_3dTrackID>`,:ref:`3dTshift <ahelp_3dTshift>`,:ref:`3dTsmooth <ahelp_3dTsmooth>`
   :ref:`3dTsort <ahelp_3dTsort>`,:ref:`3dTsplit4D <ahelp_3dTsplit4D>`,:ref:`3dTstat <ahelp_3dTstat>`
   :ref:`3dTto1D <ahelp_3dTto1D>`,:ref:`3dTwotoComplex <ahelp_3dTwotoComplex>`,:ref:`3dUndump <ahelp_3dUndump>`
   :ref:`3dUnifize <ahelp_3dUnifize>`,:ref:`3dUpsample <ahelp_3dUpsample>`,:ref:`3dVecRGB_to_HSL <ahelp_3dVecRGB_to_HSL>`
   :ref:`3dVol2Surf <ahelp_3dVol2Surf>`,:ref:`3dWarp <ahelp_3dWarp>`,:ref:`3dWarpDrive <ahelp_3dWarpDrive>`
   :ref:`3dWilcoxon <ahelp_3dWilcoxon>`,:ref:`3dWinsor <ahelp_3dWinsor>`,:ref:`3dXClustSim <ahelp_3dXClustSim>`
   :ref:`3dXYZcat <ahelp_3dXYZcat>`,:ref:`3dZcat <ahelp_3dZcat>`,:ref:`3dZcutup <ahelp_3dZcutup>`
   :ref:`3dZeropad <ahelp_3dZeropad>`,:ref:`3dZipperZapper <ahelp_3dZipperZapper>`,:ref:`3dZregrid <ahelp_3dZregrid>`
   :ref:`3danisosmooth <ahelp_3danisosmooth>`,:ref:`3daxialize <ahelp_3daxialize>`,:ref:`3dbucket <ahelp_3dbucket>`
   :ref:`3dcalc <ahelp_3dcalc>`,:ref:`3dclust <ahelp_3dclust>`,:ref:`3dcopy <ahelp_3dcopy>`
   :ref:`3ddelay <ahelp_3ddelay>`,:ref:`3ddot <ahelp_3ddot>`,:ref:`3ddot_beta <ahelp_3ddot_beta>`
   :ref:`3dedge3 <ahelp_3dedge3>`,:ref:`3dedgedog <ahelp_3dedgedog>`,:ref:`3dfim+ <ahelp_3dfim+>`
   :ref:`3dfractionize <ahelp_3dfractionize>`,:ref:`3dhistog <ahelp_3dhistog>`,:ref:`3dinfill <ahelp_3dinfill>`
   :ref:`3dinfo <ahelp_3dinfo>`,:ref:`3dkmeans <ahelp_3dkmeans>`,:ref:`3dmaskSVD <ahelp_3dmaskSVD>`
   :ref:`3dmask_tool <ahelp_3dmask_tool>`,:ref:`3dmaskave <ahelp_3dmaskave>`,:ref:`3dmaskdump <ahelp_3dmaskdump>`
   :ref:`3dmatcalc <ahelp_3dmatcalc>`,:ref:`3dmatmult <ahelp_3dmatmult>`,:ref:`3dmaxdisp <ahelp_3dmaxdisp>`
   :ref:`3dmaxima <ahelp_3dmaxima>`,:ref:`3dmerge <ahelp_3dmerge>`,:ref:`3dnewid <ahelp_3dnewid>`
   :ref:`3dnvals <ahelp_3dnvals>`,:ref:`3dpc <ahelp_3dpc>`,:ref:`3drefit <ahelp_3drefit>`
   :ref:`3drename <ahelp_3drename>`,:ref:`3dresample <ahelp_3dresample>`,:ref:`3dretroicor <ahelp_3dretroicor>`
   :ref:`3drotate <ahelp_3drotate>`,:ref:`3dsvm <ahelp_3dsvm>`,:ref:`3dsvm_linpredict <ahelp_3dsvm_linpredict>`
   :ref:`3dtoXdataset <ahelp_3dtoXdataset>`,:ref:`3dttest++ <ahelp_3dttest++>`,:ref:`3dvolreg <ahelp_3dvolreg>`
   :ref:`4swap <ahelp_4swap>`,:ref:`@1dDiffMag <ahelp_@1dDiffMag>`,:ref:`@2dwarper <ahelp_@2dwarper>`
   :ref:`@2dwarper.Allin <ahelp_@2dwarper.Allin>`,:ref:`@4Daverage <ahelp_@4Daverage>`,:ref:`@ANATICOR <ahelp_@ANATICOR>`
   :ref:`@AddEdge <ahelp_@AddEdge>`,:ref:`@AfniEnv <ahelp_@AfniEnv>`,:ref:`@AfniOrient2RAImap <ahelp_@AfniOrient2RAImap>`
   :ref:`@AfniOrientSign <ahelp_@AfniOrientSign>`,:ref:`@Align_Centers <ahelp_@Align_Centers>`,:ref:`@Atlasize <ahelp_@Atlasize>`
   :ref:`@Center_Distance <ahelp_@Center_Distance>`,:ref:`@CheckForAfniDset <ahelp_@CheckForAfniDset>`,:ref:`@ClustExp_CatLab <ahelp_@ClustExp_CatLab>`
   :ref:`@ClustExp_run_shiny <ahelp_@ClustExp_run_shiny>`,:ref:`@CommandGlobb <ahelp_@CommandGlobb>`,:ref:`@DO.examples <ahelp_@DO.examples>`
   :ref:`@DeblankFileNames <ahelp_@DeblankFileNames>`,:ref:`@DiceMetric <ahelp_@DiceMetric>`,:ref:`@DriveAfni <ahelp_@DriveAfni>`
   :ref:`@DriveSuma <ahelp_@DriveSuma>`,:ref:`@ElectroGrid <ahelp_@ElectroGrid>`,:ref:`@ExamineGenFeatDists <ahelp_@ExamineGenFeatDists>`
   :ref:`@FS_roi_label <ahelp_@FS_roi_label>`,:ref:`@FSlabel2dset <ahelp_@FSlabel2dset>`,:ref:`@FindAfniDsetPath <ahelp_@FindAfniDsetPath>`
   :ref:`@FromRAI <ahelp_@FromRAI>`,:ref:`@FullPath <ahelp_@FullPath>`,:ref:`@GetAfniBin <ahelp_@GetAfniBin>`
   :ref:`@GetAfniDims <ahelp_@GetAfniDims>`,:ref:`@GetAfniID <ahelp_@GetAfniID>`,:ref:`@GetAfniOrient <ahelp_@GetAfniOrient>`
   :ref:`@GetAfniPrefix <ahelp_@GetAfniPrefix>`,:ref:`@GetAfniRes <ahelp_@GetAfniRes>`,:ref:`@GetAfniView <ahelp_@GetAfniView>`
   :ref:`@GradFlipTest <ahelp_@GradFlipTest>`,:ref:`@Install_3dPFM_Demo <ahelp_@Install_3dPFM_Demo>`,:ref:`@Install_APMULTI_Demo1_rest <ahelp_@Install_APMULTI_Demo1_rest>`
   :ref:`@Install_APMULTI_Demo2_realtime <ahelp_@Install_APMULTI_Demo2_realtime>`,:ref:`@Install_AfniRetinoDemo <ahelp_@Install_AfniRetinoDemo>`,:ref:`@Install_ClustScat_Demo <ahelp_@Install_ClustScat_Demo>`
   :ref:`@Install_D99_macaque <ahelp_@Install_D99_macaque>`,:ref:`@Install_DBSproc <ahelp_@Install_DBSproc>`,:ref:`@Install_FATCAT_DEMO <ahelp_@Install_FATCAT_DEMO>`
   :ref:`@Install_FATCAT_DEMO2 <ahelp_@Install_FATCAT_DEMO2>`,:ref:`@Install_FATMVM_DEMO <ahelp_@Install_FATMVM_DEMO>`,:ref:`@Install_IBT_DATASETS <ahelp_@Install_IBT_DATASETS>`
   :ref:`@Install_InstaCorr_Demo <ahelp_@Install_InstaCorr_Demo>`,:ref:`@Install_MACAQUE_DEMO <ahelp_@Install_MACAQUE_DEMO>`,:ref:`@Install_MACAQUE_DEMO_REST <ahelp_@Install_MACAQUE_DEMO_REST>`
   :ref:`@Install_MBM_Marmoset <ahelp_@Install_MBM_Marmoset>`,:ref:`@Install_MEICA_Demo <ahelp_@Install_MEICA_Demo>`,:ref:`@Install_NIH_Marmoset <ahelp_@Install_NIH_Marmoset>`
   :ref:`@Install_NMT <ahelp_@Install_NMT>`,:ref:`@Install_RAT_DEMO_REST <ahelp_@Install_RAT_DEMO_REST>`,:ref:`@Install_RSFMRI_Motion_Group_Demo <ahelp_@Install_RSFMRI_Motion_Group_Demo>`
   :ref:`@Install_SAM_marmoset <ahelp_@Install_SAM_marmoset>`,:ref:`@Install_SURFLAYERS_DEMO1 <ahelp_@Install_SURFLAYERS_DEMO1>`,:ref:`@Install_TSrestMovieDemo <ahelp_@Install_TSrestMovieDemo>`
   :ref:`@IsoMasks <ahelp_@IsoMasks>`,:ref:`@MakeLabelTable <ahelp_@MakeLabelTable>`,:ref:`@NoExt <ahelp_@NoExt>`
   :ref:`@NoPound <ahelp_@NoPound>`,:ref:`@NoisySkullStrip <ahelp_@NoisySkullStrip>`,:ref:`@Purify_1D <ahelp_@Purify_1D>`
   :ref:`@Quiet_Talkers <ahelp_@Quiet_Talkers>`,:ref:`@ROI_Corr_Mat <ahelp_@ROI_Corr_Mat>`,:ref:`@ROI_decluster <ahelp_@ROI_decluster>`
   :ref:`@ROI_modal_grow <ahelp_@ROI_modal_grow>`,:ref:`@R_funclist <ahelp_@R_funclist>`,:ref:`@RenamePanga <ahelp_@RenamePanga>`
   :ref:`@Reorder <ahelp_@Reorder>`,:ref:`@RetinoProc <ahelp_@RetinoProc>`,:ref:`@SSwarper <ahelp_@SSwarper>`
   :ref:`@SUMA_AlignToExperiment <ahelp_@SUMA_AlignToExperiment>`,:ref:`@SUMA_FSvolToBRIK <ahelp_@SUMA_FSvolToBRIK>`,:ref:`@SUMA_Make_Spec_Caret <ahelp_@SUMA_Make_Spec_Caret>`
   :ref:`@SUMA_Make_Spec_FS <ahelp_@SUMA_Make_Spec_FS>`,:ref:`@SUMA_Make_Spec_SF <ahelp_@SUMA_Make_Spec_SF>`,:ref:`@SUMA_renumber_FS <ahelp_@SUMA_renumber_FS>`
   :ref:`@ScaleVolume <ahelp_@ScaleVolume>`,:ref:`@ScriptCheck <ahelp_@ScriptCheck>`,:ref:`@Shift_Volume <ahelp_@Shift_Volume>`
   :ref:`@ShowDynamicRange <ahelp_@ShowDynamicRange>`,:ref:`@SkullStrip_TouchUp <ahelp_@SkullStrip_TouchUp>`,:ref:`@Spharm.examples <ahelp_@Spharm.examples>`
   :ref:`@SurfSmooth.HEAT_07.examples <ahelp_@SurfSmooth.HEAT_07.examples>`,:ref:`@T1scale <ahelp_@T1scale>`,:ref:`@TimeDiff <ahelp_@TimeDiff>`
   :ref:`@ToRAI <ahelp_@ToRAI>`,:ref:`@VolCenter <ahelp_@VolCenter>`,:ref:`@afni.run.me <ahelp_@afni.run.me>`
   :ref:`@afni_R_package_install <ahelp_@afni_R_package_install>`,:ref:`@afni_refacer_make_master <ahelp_@afni_refacer_make_master>`,:ref:`@afni_refacer_make_master_addendum <ahelp_@afni_refacer_make_master_addendum>`
   :ref:`@afni_refacer_make_onebigA12 <ahelp_@afni_refacer_make_onebigA12>`,:ref:`@afni_refacer_run <ahelp_@afni_refacer_run>`,:ref:`@align_partial_oblique <ahelp_@align_partial_oblique>`
   :ref:`@animal_warper <ahelp_@animal_warper>`,:ref:`@auto_tlrc <ahelp_@auto_tlrc>`,:ref:`@build_afni_Xlib <ahelp_@build_afni_Xlib>`
   :ref:`@chauffeur_afni <ahelp_@chauffeur_afni>`,:ref:`@clean_help_dir <ahelp_@clean_help_dir>`,:ref:`@clip_volume <ahelp_@clip_volume>`
   :ref:`@compute_OC_weights <ahelp_@compute_OC_weights>`,:ref:`@compute_gcor <ahelp_@compute_gcor>`,:ref:`@demo_prompt <ahelp_@demo_prompt>`
   :ref:`@diff.files <ahelp_@diff.files>`,:ref:`@diff.tree <ahelp_@diff.tree>`,:ref:`@djunct_4d_imager <ahelp_@djunct_4d_imager>`
   :ref:`@djunct_4d_slices_to_3d_vol <ahelp_@djunct_4d_slices_to_3d_vol>`,:ref:`@djunct_anonymize <ahelp_@djunct_anonymize>`,:ref:`@djunct_dwi_selector.tcsh <ahelp_@djunct_dwi_selector.tcsh>`
   :ref:`@djunct_edgy_align_check <ahelp_@djunct_edgy_align_check>`,:ref:`@djunct_glue_imgs_vert <ahelp_@djunct_glue_imgs_vert>`,:ref:`@djunct_json_value.py <ahelp_@djunct_json_value.py>`
   :ref:`@djunct_modal_smoothing_with_rep <ahelp_@djunct_modal_smoothing_with_rep>`,:ref:`@djunct_montage_coordinator <ahelp_@djunct_montage_coordinator>`,:ref:`@djunct_overlap_check <ahelp_@djunct_overlap_check>`
   :ref:`@djunct_slice_space <ahelp_@djunct_slice_space>`,:ref:`@djunct_ssw_intermed_edge_imgs <ahelp_@djunct_ssw_intermed_edge_imgs>`,:ref:`@djunct_vol_3slice_select <ahelp_@djunct_vol_3slice_select>`
   :ref:`@escape- <ahelp_@escape->`,:ref:`@extract_meica_ortvec <ahelp_@extract_meica_ortvec>`,:ref:`@fast_roi <ahelp_@fast_roi>`
   :ref:`@fat_tract_colorize <ahelp_@fat_tract_colorize>`,:ref:`@fix_FSsphere <ahelp_@fix_FSsphere>`,:ref:`@float_fix <ahelp_@float_fix>`
   :ref:`@get.afni.version <ahelp_@get.afni.version>`,:ref:`@global_parse <ahelp_@global_parse>`,:ref:`@grayplot <ahelp_@grayplot>`
   :ref:`@help.AFNI <ahelp_@help.AFNI>`,:ref:`@isOblique <ahelp_@isOblique>`,:ref:`@make_plug_diff <ahelp_@make_plug_diff>`
   :ref:`@measure_bb_thick <ahelp_@measure_bb_thick>`,:ref:`@measure_erosion_thick <ahelp_@measure_erosion_thick>`,:ref:`@measure_in2out <ahelp_@measure_in2out>`
   :ref:`@move.to.series.dirs <ahelp_@move.to.series.dirs>`,:ref:`@np <ahelp_@np>`,:ref:`@parse_afni_name <ahelp_@parse_afni_name>`
   :ref:`@parse_name <ahelp_@parse_name>`,:ref:`@radial_correlate <ahelp_@radial_correlate>`,:ref:`@simulate_motion <ahelp_@simulate_motion>`
   :ref:`@snapshot_volreg <ahelp_@snapshot_volreg>`,:ref:`@statauxcode <ahelp_@statauxcode>`,:ref:`@suma_acknowledge <ahelp_@suma_acknowledge>`
   :ref:`@suma_reprefixize_spec <ahelp_@suma_reprefixize_spec>`,:ref:`@surf_to_vol_spackle <ahelp_@surf_to_vol_spackle>`,:ref:`@thickness_master <ahelp_@thickness_master>`
   :ref:`@toMNI_Awarp <ahelp_@toMNI_Awarp>`,:ref:`@toMNI_Qwarpar <ahelp_@toMNI_Qwarpar>`,:ref:`@update.afni.binaries <ahelp_@update.afni.binaries>`
   :ref:`@xyz_to_ijk <ahelp_@xyz_to_ijk>`,:ref:`AFNI_Batch_R <ahelp_AFNI_Batch_R>`,:ref:`AnalyzeTrace <ahelp_AnalyzeTrace>`
   :ref:`BayesianGroupAna.py <ahelp_BayesianGroupAna.py>`,:ref:`BrainSkin <ahelp_BrainSkin>`,:ref:`ClustExp_HistTable.py <ahelp_ClustExp_HistTable.py>`
   :ref:`ClustExp_StatParse.py <ahelp_ClustExp_StatParse.py>`,:ref:`CompareSurfaces <ahelp_CompareSurfaces>`,:ref:`ConvertDset <ahelp_ConvertDset>`
   :ref:`ConvertSurface <ahelp_ConvertSurface>`,:ref:`ConvexHull <ahelp_ConvexHull>`,:ref:`CreateIcosahedron <ahelp_CreateIcosahedron>`
   :ref:`DTIStudioFibertoSegments <ahelp_DTIStudioFibertoSegments>`,:ref:`Dimon <ahelp_Dimon>`,:ref:`DriveSuma <ahelp_DriveSuma>`
   :ref:`ExamineXmat <ahelp_ExamineXmat>`,:ref:`FATCAT_matplot <ahelp_FATCAT_matplot>`,:ref:`FIRdesign <ahelp_FIRdesign>`
   :ref:`FSread_annot <ahelp_FSread_annot>`,:ref:`GLTsymtest <ahelp_GLTsymtest>`,:ref:`HalloSuma <ahelp_HalloSuma>`
   :ref:`InstaTract <ahelp_InstaTract>`,:ref:`IsoSurface <ahelp_IsoSurface>`,:ref:`MBA <ahelp_MBA>`
   :ref:`MakeColorMap <ahelp_MakeColorMap>`,:ref:`MapIcosahedron <ahelp_MapIcosahedron>`,:ref:`PTA <ahelp_PTA>`
   :ref:`ParseName <ahelp_ParseName>`,:ref:`RBA <ahelp_RBA>`,:ref:`ROI2dataset <ahelp_ROI2dataset>`
   :ref:`ROIgrow <ahelp_ROIgrow>`,:ref:`RSFgen <ahelp_RSFgen>`,:ref:`RetroTS.py <ahelp_RetroTS.py>`
   :ref:`SUMA_glxdino <ahelp_SUMA_glxdino>`,:ref:`SUMA_paperplane <ahelp_SUMA_paperplane>`,:ref:`SUMA_pixmap2eps <ahelp_SUMA_pixmap2eps>`
   :ref:`SampBias <ahelp_SampBias>`,:ref:`ScaleToMap <ahelp_ScaleToMap>`,:ref:`SpharmDeco <ahelp_SpharmDeco>`
   :ref:`SpharmReco <ahelp_SpharmReco>`,:ref:`Surf2VolCoord <ahelp_Surf2VolCoord>`,:ref:`SurfClust <ahelp_SurfClust>`
   :ref:`SurfDist <ahelp_SurfDist>`,:ref:`SurfDsetInfo <ahelp_SurfDsetInfo>`,:ref:`SurfExtrema <ahelp_SurfExtrema>`
   :ref:`SurfFWHM <ahelp_SurfFWHM>`,:ref:`SurfInfo <ahelp_SurfInfo>`,:ref:`SurfLayers <ahelp_SurfLayers>`
   :ref:`SurfLocalstat <ahelp_SurfLocalstat>`,:ref:`SurfMeasures <ahelp_SurfMeasures>`,:ref:`SurfMesh <ahelp_SurfMesh>`
   :ref:`SurfPatch <ahelp_SurfPatch>`,:ref:`SurfQual <ahelp_SurfQual>`,:ref:`SurfRetinoMap <ahelp_SurfRetinoMap>`
   :ref:`SurfSmooth <ahelp_SurfSmooth>`,:ref:`SurfToSurf <ahelp_SurfToSurf>`,:ref:`SurfaceMetrics <ahelp_SurfaceMetrics>`
   :ref:`TRR <ahelp_TRR>`,:ref:`Vecwarp <ahelp_Vecwarp>`,:ref:`abids_json_info.py <ahelp_abids_json_info.py>`
   :ref:`abids_json_tool.py <ahelp_abids_json_tool.py>`,:ref:`abids_tool.py <ahelp_abids_tool.py>`,:ref:`adjunct_apqc_tsnr_general <ahelp_adjunct_apqc_tsnr_general>`
   :ref:`adjunct_atlas_points_to_labeltable <ahelp_adjunct_atlas_points_to_labeltable>`,:ref:`adjunct_aw_tableize_roi_info.py <ahelp_adjunct_aw_tableize_roi_info.py>`,:ref:`adjunct_calc_mont_dims.py <ahelp_adjunct_calc_mont_dims.py>`
   :ref:`adjunct_cbar_out <ahelp_adjunct_cbar_out>`,:ref:`adjunct_combine_str.py <ahelp_adjunct_combine_str.py>`,:ref:`adjunct_deob_around_origin <ahelp_adjunct_deob_around_origin>`
   :ref:`adjunct_is_label.py <ahelp_adjunct_is_label.py>`,:ref:`adjunct_make_script_and_rst.py <ahelp_adjunct_make_script_and_rst.py>`,:ref:`adjunct_middle_pair_mask <ahelp_adjunct_middle_pair_mask>`
   :ref:`adjunct_select_str.py <ahelp_adjunct_select_str.py>`,:ref:`adjunct_simplify_cost.py <ahelp_adjunct_simplify_cost.py>`,:ref:`adjunct_suma_fs_mask_and_qc <ahelp_adjunct_suma_fs_mask_and_qc>`
   :ref:`adjunct_suma_fs_roi_info <ahelp_adjunct_suma_fs_roi_info>`,:ref:`adjunct_tort_plot_dp_align <ahelp_adjunct_tort_plot_dp_align>`,:ref:`adjunct_tort_read_dp_align.py <ahelp_adjunct_tort_read_dp_align.py>`
   :ref:`adwarp <ahelp_adwarp>`,:ref:`afni <ahelp_afni>`,:ref:`afni_check_omp <ahelp_afni_check_omp>`
   :ref:`afni_history <ahelp_afni_history>`,:ref:`afni_open <ahelp_afni_open>`,:ref:`afni_proc.py <ahelp_afni_proc.py>`
   :ref:`afni_python_wrapper.py <ahelp_afni_python_wrapper.py>`,:ref:`afni_run_R <ahelp_afni_run_R>`,:ref:`afni_skeleton.py <ahelp_afni_skeleton.py>`
   :ref:`afni_system_check.py <ahelp_afni_system_check.py>`,:ref:`afni_vcheck <ahelp_afni_vcheck>`,:ref:`aiv <ahelp_aiv>`
   :ref:`align_epi_anat.py <ahelp_align_epi_anat.py>`,:ref:`ap_run_simple_rest.tcsh <ahelp_ap_run_simple_rest.tcsh>`,:ref:`ap_run_simple_rest_me.tcsh <ahelp_ap_run_simple_rest_me.tcsh>`
   :ref:`apqc_make_html.py <ahelp_apqc_make_html.py>`,:ref:`apqc_make_tcsh.py <ahelp_apqc_make_tcsh.py>`,:ref:`apsearch <ahelp_apsearch>`
   :ref:`auto_warp.py <ahelp_auto_warp.py>`,:ref:`balloon <ahelp_balloon>`,:ref:`bayes_view <ahelp_bayes_view>`
   :ref:`build_afni.py <ahelp_build_afni.py>`,:ref:`byteorder <ahelp_byteorder>`,:ref:`cat_matvec <ahelp_cat_matvec>`
   :ref:`ccalc <ahelp_ccalc>`,:ref:`cdf <ahelp_cdf>`,:ref:`chauffeur_map_rois <ahelp_chauffeur_map_rois>`
   :ref:`cifti_tool <ahelp_cifti_tool>`,:ref:`cjpeg <ahelp_cjpeg>`,:ref:`colorbar_tool.py <ahelp_colorbar_tool.py>`
   :ref:`column_cat <ahelp_column_cat>`,:ref:`compute_ROI_stats.tcsh <ahelp_compute_ROI_stats.tcsh>`,:ref:`convert_cdiflist_to_grads.py <ahelp_convert_cdiflist_to_grads.py>`
   :ref:`count <ahelp_count>`,:ref:`count_afni <ahelp_count_afni>`,:ref:`dcm2niix_afni <ahelp_dcm2niix_afni>`
   :ref:`desphinxify <ahelp_desphinxify>`,:ref:`dicom_hdr <ahelp_dicom_hdr>`,:ref:`dicom_hinfo <ahelp_dicom_hinfo>`
   :ref:`dicom_to_raw <ahelp_dicom_to_raw>`,:ref:`djpeg <ahelp_djpeg>`,:ref:`dsetstat2p <ahelp_dsetstat2p>`
   :ref:`eg_main_chrono.py <ahelp_eg_main_chrono.py>`,:ref:`epi_b0_correct.py <ahelp_epi_b0_correct.py>`,:ref:`fat_mat2d_plot.py <ahelp_fat_mat2d_plot.py>`
   :ref:`fat_mat_sel.py <ahelp_fat_mat_sel.py>`,:ref:`fat_mat_tableize.py <ahelp_fat_mat_tableize.py>`,:ref:`fat_mvm_gridconv.py <ahelp_fat_mvm_gridconv.py>`
   :ref:`fat_mvm_prep.py <ahelp_fat_mvm_prep.py>`,:ref:`fat_mvm_scripter.py <ahelp_fat_mvm_scripter.py>`,:ref:`fat_proc_align_anat_pair <ahelp_fat_proc_align_anat_pair>`
   :ref:`fat_proc_axialize_anat <ahelp_fat_proc_axialize_anat>`,:ref:`fat_proc_connec_vis <ahelp_fat_proc_connec_vis>`,:ref:`fat_proc_convert_dcm_anat <ahelp_fat_proc_convert_dcm_anat>`
   :ref:`fat_proc_convert_dcm_dwis <ahelp_fat_proc_convert_dcm_dwis>`,:ref:`fat_proc_decmap <ahelp_fat_proc_decmap>`,:ref:`fat_proc_dwi_to_dt <ahelp_fat_proc_dwi_to_dt>`
   :ref:`fat_proc_filter_dwis <ahelp_fat_proc_filter_dwis>`,:ref:`fat_proc_imit2w_from_t1w <ahelp_fat_proc_imit2w_from_t1w>`,:ref:`fat_proc_map_to_dti <ahelp_fat_proc_map_to_dti>`
   :ref:`fat_proc_select_vols <ahelp_fat_proc_select_vols>`,:ref:`fat_roi_row.py <ahelp_fat_roi_row.py>`,:ref:`fdrval <ahelp_fdrval>`
   :ref:`fftest <ahelp_fftest>`,:ref:`file_tool <ahelp_file_tool>`,:ref:`fim2 <ahelp_fim2>`
   :ref:`find_variance_lines.tcsh <ahelp_find_variance_lines.tcsh>`,:ref:`float_scan <ahelp_float_scan>`,:ref:`from3d <ahelp_from3d>`
   :ref:`gen_cluster_table <ahelp_gen_cluster_table>`,:ref:`gen_epi_review.py <ahelp_gen_epi_review.py>`,:ref:`gen_group_command.py <ahelp_gen_group_command.py>`
   :ref:`gen_ss_review_scripts.py <ahelp_gen_ss_review_scripts.py>`,:ref:`gen_ss_review_table.py <ahelp_gen_ss_review_table.py>`,:ref:`get_afni_model_PRF <ahelp_get_afni_model_PRF>`
   :ref:`get_afni_model_PRF_6 <ahelp_get_afni_model_PRF_6>`,:ref:`get_afni_model_PRF_6_BAD <ahelp_get_afni_model_PRF_6_BAD>`,:ref:`get_afni_model_PRF_DN <ahelp_get_afni_model_PRF_DN>`
   :ref:`gifti_tool <ahelp_gifti_tool>`,:ref:`gtkyd_check <ahelp_gtkyd_check>`,:ref:`gtkyd_check.py <ahelp_gtkyd_check.py>`
   :ref:`help_format <ahelp_help_format>`,:ref:`im2niml <ahelp_im2niml>`,:ref:`images_equal <ahelp_images_equal>`
   :ref:`imand <ahelp_imand>`,:ref:`imaver <ahelp_imaver>`,:ref:`imcalc <ahelp_imcalc>`
   :ref:`imcat <ahelp_imcat>`,:ref:`imcutup <ahelp_imcutup>`,:ref:`imdump <ahelp_imdump>`
   :ref:`immask <ahelp_immask>`,:ref:`imreg <ahelp_imreg>`,:ref:`imrotate <ahelp_imrotate>`
   :ref:`imstack <ahelp_imstack>`,:ref:`imstat <ahelp_imstat>`,:ref:`imupsam <ahelp_imupsam>`
   :ref:`init_user_dotfiles.py <ahelp_init_user_dotfiles.py>`,:ref:`inspec <ahelp_inspec>`,:ref:`lesion_align <ahelp_lesion_align>`
   :ref:`make_pq_script.py <ahelp_make_pq_script.py>`,:ref:`make_random_timing.py <ahelp_make_random_timing.py>`,:ref:`make_stim_times.py <ahelp_make_stim_times.py>`
   :ref:`map_TrackID <ahelp_map_TrackID>`,:ref:`map_ap_to_deriv.py <ahelp_map_ap_to_deriv.py>`,:ref:`meica.py <ahelp_meica.py>`
   :ref:`mycat <ahelp_mycat>`,:ref:`myget <ahelp_myget>`,:ref:`neuro_deconvolve.py <ahelp_neuro_deconvolve.py>`
   :ref:`nicat <ahelp_nicat>`,:ref:`niccc <ahelp_niccc>`,:ref:`nifti1_tool <ahelp_nifti1_tool>`
   :ref:`nifti_tool <ahelp_nifti_tool>`,:ref:`niml_feedme <ahelp_niml_feedme>`,:ref:`niprobe <ahelp_niprobe>`
   :ref:`nsize <ahelp_nsize>`,:ref:`open_apqc.py <ahelp_open_apqc.py>`,:ref:`p2dsetstat <ahelp_p2dsetstat>`
   :ref:`parse_fs_lt_log.py <ahelp_parse_fs_lt_log.py>`,:ref:`physio_calc.py <ahelp_physio_calc.py>`,:ref:`plugout_drive <ahelp_plugout_drive>`
   :ref:`plugout_ijk <ahelp_plugout_ijk>`,:ref:`plugout_tt <ahelp_plugout_tt>`,:ref:`plugout_tta <ahelp_plugout_tta>`
   :ref:`prompt_popup <ahelp_prompt_popup>`,:ref:`prompt_user <ahelp_prompt_user>`,:ref:`python_module_test.py <ahelp_python_module_test.py>`
   :ref:`quick.alpha.vals.py <ahelp_quick.alpha.vals.py>`,:ref:`quickspec <ahelp_quickspec>`,:ref:`quickspecSL <ahelp_quickspecSL>`
   :ref:`quotize <ahelp_quotize>`,:ref:`rPkgsInstall <ahelp_rPkgsInstall>`,:ref:`rbox <ahelp_rbox>`
   :ref:`read_matlab_files.py <ahelp_read_matlab_files.py>`,:ref:`realtime_receiver.py <ahelp_realtime_receiver.py>`,:ref:`rmz <ahelp_rmz>`
   :ref:`roi_stats_warnings.py <ahelp_roi_stats_warnings.py>`,:ref:`rotcom <ahelp_rotcom>`,:ref:`rtfeedme <ahelp_rtfeedme>`
   :ref:`serial_helper <ahelp_serial_helper>`,:ref:`sfim <ahelp_sfim>`,:ref:`slow_surf_clustsim.py <ahelp_slow_surf_clustsim.py>`
   :ref:`sswarper2 <ahelp_sswarper2>`,:ref:`stimband <ahelp_stimband>`,:ref:`stouffer <ahelp_stouffer>`
   :ref:`strblast <ahelp_strblast>`,:ref:`suma <ahelp_suma>`,:ref:`suma_change_spec <ahelp_suma_change_spec>`
   :ref:`tedana_wrapper.py <ahelp_tedana_wrapper.py>`,:ref:`test_afni_prog_help.tcsh <ahelp_test_afni_prog_help.tcsh>`,:ref:`tfim <ahelp_tfim>`
   :ref:`timing_tool.py <ahelp_timing_tool.py>`,:ref:`to3d <ahelp_to3d>`,:ref:`tokens <ahelp_tokens>`
   :ref:`uber_align_test.py <ahelp_uber_align_test.py>`,:ref:`uber_proc.py <ahelp_uber_proc.py>`,:ref:`uber_skel.py <ahelp_uber_skel.py>`
   :ref:`uber_subject.py <ahelp_uber_subject.py>`,:ref:`uber_ttest.py <ahelp_uber_ttest.py>`,:ref:`unWarpEPI.py <ahelp_unWarpEPI.py>`
   :ref:`uniq_images <ahelp_uniq_images>`,:ref:`waver <ahelp_waver>`,:ref:`whereami <ahelp_whereami>`
   :ref:`whereami_afni <ahelp_whereami_afni>`,:ref:`whirlgif <ahelp_whirlgif>`,:ref:`xmat_tool.py <ahelp_xmat_tool.py>`


.. _programs_main_pdfman:

Links to program manuals
----------------------------

This is a list of all AFNI program manuals, which were written in
ancient times in elvish runes.  These are the few that have been
translated to modern(ish) human speak.

It is possible that some of these manuals refer to programs that are
no longer in circulation, typically having been deprecated for a newer
one.  The "classified" list of program helps
:ref:`HERE<edu_class_prog>`\, contains information on such
deprecations and pointers to the more modern version.

.. csv-table::
   :width: 100%

   `1dplot.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/1dplot.pdf>`_,`24swap.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/24swap.pdf>`_,`2dImReg.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/2dImReg.pdf>`_
   `2swap.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/2swap.pdf>`_,`3dANOVA2.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dANOVA2.pdf>`_,`3dANOVA3.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dANOVA3.pdf>`_
   `3dANOVA.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dANOVA.pdf>`_,`3daxialize.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3daxialize.pdf>`_,`3dbuc2fim.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dbuc2fim.pdf>`_
   `3dbucket.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dbucket.pdf>`_,`3dcalc.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dcalc.pdf>`_,`3dclust.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dclust.pdf>`_
   `3dcolon.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dcolon.pdf>`_,`3dDeconvolve.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dDeconvolve.pdf>`_,`3ddup.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3ddup.pdf>`_
   `3dExtrema.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dExtrema.pdf>`_,`3dFDR.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dFDR.pdf>`_,`3dfim+.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dfim+.pdf>`_
   `3dfim.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dfim.pdf>`_,`3dfractionize.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dfractionize.pdf>`_,`3dFriedman.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dFriedman.pdf>`_
   `3dFWHM.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dFWHM.pdf>`_,`3dhistog.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dhistog.pdf>`_,`3dinfo.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dinfo.pdf>`_
   `3dIntracranial.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dIntracranial.pdf>`_,`3dKruskalWallis.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dKruskalWallis.pdf>`_,`3dMannWhitney.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dMannWhitney.pdf>`_
   `3dmaskave.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dmaskave.pdf>`_,`3dmerge.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dmerge.pdf>`_,`3dnewid.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dnewid.pdf>`_
   `3dNLfim.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dNLfim.pdf>`_,`3dnoise.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dnoise.pdf>`_,`3dnvals.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dnvals.pdf>`_
   `3dpc.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dpc.pdf>`_,`3dproject.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dproject.pdf>`_,`3drefit.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3drefit.pdf>`_
   `3dRegAnam.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dRegAnam.pdf>`_,`3dRegAna.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dRegAna.pdf>`_,`3drotate.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3drotate.pdf>`_
   `3dStatClust.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dStatClust.pdf>`_,`3dTcat.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dTcat.pdf>`_,`3dTSgen.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dTSgen.pdf>`_
   `3dTsmooth.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dTsmooth.pdf>`_,`3dttest.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dttest.pdf>`_,`3dvolreg.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dvolreg.pdf>`_
   `3dWavelets.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dWavelets.pdf>`_,`3dWilcoxon.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3dWilcoxon.pdf>`_,`3T_toafni.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/3T_toafni.pdf>`_
   `4swap.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/4swap.pdf>`_,`abut.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/abut.pdf>`_,`adwarp.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/adwarp.pdf>`_
   `AlphaSim_fig.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/AlphaSim_fig.pdf>`_,`AlphaSim.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/AlphaSim.pdf>`_,`ANOVAm.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/ANOVAm.pdf>`_
   `buckets.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/buckets.pdf>`_,`byteorder.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/byteorder.pdf>`_,`ccalc.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/ccalc.pdf>`_
   `cdf.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/cdf.pdf>`_,`count.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/count.pdf>`_,`Deconvolvem.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/Deconvolvem.pdf>`_
   `FD2.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/FD2.pdf>`_,`fim2.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/fim2.pdf>`_,`float_scan.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/float_scan.pdf>`_
   `from3d.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/from3d.pdf>`_,`ftosh.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/ftosh.pdf>`_,`imand.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imand.pdf>`_
   `imaver.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imaver.pdf>`_,`imcalc.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imcalc.pdf>`_,`imdump.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imdump.pdf>`_
   `immask.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/immask.pdf>`_,`imreg.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imreg.pdf>`_,`imrotate.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imrotate.pdf>`_
   `imstack.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imstack.pdf>`_,`imstat.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imstat.pdf>`_,`imupsam.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/imupsam.pdf>`_
   `mritopgm.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/mritopgm.pdf>`_,`Nonparametric.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/Nonparametric.pdf>`_,`nsize.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/nsize.pdf>`_
   `p2t.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/p2t.pdf>`_,`RSFgen.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/RSFgen.pdf>`_,`sfim.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/sfim.pdf>`_
   `sqwave.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/sqwave.pdf>`_,`Table.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/Table.pdf>`_,`tfim.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/tfim.pdf>`_
   `to3d.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/to3d.pdf>`_,`waver.pdf <https://afni.nimh.nih.gov/pub/dist/doc/manual/waver.pdf>`_,