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]
1dApar2mat 1dAstrip 1dBandpass 1dBport
1dcat 1dCorrelate @1dDiffMag 1ddot
1dDW_Grad_o_Mat 1dDW_Grad_o_Mat++ 1deval 1dfft
1dFlagMotion 1dgenARMA11 1dgrayplot 1dMarry
1dmatcalc 1dNLfit 1dnorm 1dplot
1dplot.py 1dRplot 1dSEM 1dsound
1dsum 1dsvd 1d_tool.py 1dtranspose
1dTsort 1dUpsample 24swap a 2dcat
2dImReg @2dwarper.Allin 2perm 2swap a
3dABoverlap 3dAFNIto3D 3dAFNItoANALYZE a 3dAFNItoMINC a
3dAFNItoNIFTI 3dAFNItoNIML 3dAFNItoRaw 3dAllineate
3dAmpToRSFC 3dANALYZEtoAFNI 3dAnatNudge a 3dAnhist a
3danisosmooth 3dANOVA 3dANOVA2 3dANOVA3
3dAttribute 3dAutobox 3dAutomask 3dAutoTcorrelate
3daxialize a 3dBallMatch 3dBandpass 3dBlurInMask
3dBlurToFWHM 3dBrainSync 3dBRAIN_VOYAGERtoAFNI 3dBrickStat
3dbuc2fim a 3dbucket 3dcalc 3dClipLevel a
3dclust 3dClustCount 3dClusterize 3dClustSim
3dCM 3dCompareAffine 3dConformist 3dConvolve
3dcopy 3dCountSpikes 3dCRUISEtoAFNI 3dDeconvolve
3dDeconvolve_f a 3dDegreeCentrality 3ddelay 3dDepthMap
3dDespike 3dDetrend 3dDFT 3dDiff
3ddot a 3ddot_beta 3dDTeig 3dDTtoDWI
3dDTtoNoisyDWI 3ddup a 3dDWItoDT 3dDWUncert
3dECM 3dedge3 3dedgedog 3dEdu_01_scale
3dEduProg 3dEigsToDT 3dEmpty 3dEntropy
3dEulerDist 3dExchange 3dExtractGroupInCorr 3dExtrema
3dFDR 3dFFT 3dfim 3dfim+
3dFourier 3dfractionize 3dFriedman 3dFWHM a
3dFWHMx 3dGenFeatureDist 3dGenPriors 3dGetrow
3dGrayplot 3dGroupInCorr 3dHist 3dhistog
3dICC 3dinfill 3dinfo 3dIntracranial a
3dInvFMRI 3dISC 3dkmeans 3dKruskalWallis
3dLFCD 3dLME 3dLMEr 3dLocalACF
3dLocalBistat 3dLocalHistog 3dLocalPV 3dLocalstat
3dLocalSVD 3dLombScargle 3dLRflip 3dLSS
3dMannWhitney 3dmaskave 3dmaskdump 3dmaskSVD
3dMaskToASCII 3dmask_tool 3dmatcalc 3dMatch
3dmatmult 3dmaxdisp 3dmaxima 3dMean
3dMedianFilter 3dMEMA 3dMEPFM 3dmerge
3dMINCtoAFNI a 3dMSE 3dMSS 3dMultiThresh
3dMVM 3dMVM_validator 3dNetCorr 3dnewid
3dNLfim 3dnoise a 3dNormalityTest 3dNotes
3dnvals 3dNwarpAdjust 3dNwarpApply 3dNwarpCalc
3dNwarpCat 3dNwarpFuncs 3dNwarpXYZ 3dOverlap
3dPAR2AFNI.pl 3dpc 3dPeriodogram 3dPFM
3dPolyfit 3dProbTrackID 3dproject a 3dPval
3dPVmap 3dQwarp 3dRank 3dRankizer
3drefit 3dRegAna 3dReHo 3dREMLfit
3drename 3dresample 3dRetinoPhase 3dretroicor
3dROIMaker 3dROIstats 3drotate 3dRowFillin
3dRprogDemo 3dRSFC 3dSeg 3dSetupGroupInCorr
3dSharpen 3dSignatures 3dSkullStrip 3dSliceNDice
3dSpaceTimeCorr 3dStatClust 3dSurf2Vol 3dSurfMask
3dsvm 3dsvm_linpredict 3dSynthesize 3dTagalign
3dTcat 3dTcorr1D 3dTcorrelate 3dTcorrMap
3dTfilter 3dTfitter 3dThreetoRGB 3dTnorm
3dTORTOISEtoHere 3dToutcount 3dtoXdataset 3dToyProg
3dTproject 3dTqual 3dTrackID 3dTRfix
3dTSgen 3dTshift 3dTsmooth 3dTsort
3dTsplit4D 3dTstat 3dttest 3dttest++
3dTto1D 3dTwotoComplex 3dUndump 3dUnifize
3dUniformize 3dUpsample 3dVecRGB_to_HSL 3dVol2Surf
3dvolreg 3dWarp a 3dWarpDrive a 3dWavelets a
3dWilcoxon 3dWinsor 3dXClustSim 3dXYZcat
3dZcat 3dZcutup 3dZeropad 3dZipperZapper
3dZregrid @4Daverage 4swap a abids_json_info.py
abids_json_tool.py abids_tool.py abut a @AddEdge
adjunct_apqc_tsnr_general adjunct_apqc_tsnr_no_mask adjunct_apqc_tsnr_with_mask adjunct_aw_tableize_roi_info.py
adjunct_calc_mont_dims.py adjunct_combine_str.py adjunct_is_label.py adjunct_make_script_and_rst.py
adjunct_select_str.py adjunct_simplify_cost.py adjunct_suma_fs_mask_and_qc adjunct_suma_fs_qc.tcsh
adjunct_suma_fs_roi_info adjunct_suma_fs_rois.tcsh adjunct_tort_plot_dp_align adjunct_tort_read_dp_align.py
adwarp afni afni_check_omp @AfniEnv
afni_history afni_open @AfniOrient2RAImap afni_proc.py
afni_python_wrapper.py @afni_refacer_make_master @afni_refacer_make_master_addendum @afni_refacer_make_onebigA12
@afni_refacer_run afni_restproc.py @afni_R_package_install @afni.run.me
afni_skeleton.py afni_system_check.py afni_vcheck aiv
@Align_Centers align_epi_anat.py @align_partial_oblique AlphaSim a
AnalyzeTrace @ANATICOR @animal_warper apqc_make_html.py
apqc_make_tcsh.py ap_run_simple_rest.tcsh apsearch @Atlasize
@auto_tlrc auto_warp.py balloon BayesianGroupAna.py
BrainSkin @build_afni_Xlib byteorder CA_EZ_atlas.csh
cat_matvec ccalc cdf @Center_Distance
@chauffeur_afni check_dset_for_fs.py @CheckForAfniDset cifti_tool
cjpeg @clean_help_dir @clip_volume @ClustExp_CatLab
ClustExp_HistTable.py @ClustExp_run_shiny ClustExp_StatParse.py column_cat
@CommandGlobb CompareSurfaces @compute_gcor @compute_OC_weights
convert_cdiflist_to_grads.py ConvertDset ConvertSurface ConvexHull
count CreateIcosahedron dcm2niix_afni @DeblankFileNames
demoExpt.py @DiceMetric dicom_hdr dicom_hinfo
dicom_to_raw @diff.files @diff.tree Dimon
Dimon1 djpeg @djunct_4d_imager @djunct_4d_slices_to_3d_vol
@djunct_anonymize @djunct_calc_mont_dims.py @djunct_combine_str.py @djunct_dwi_selector.tcsh
@djunct_edgy_align_check @djunct_glue_imgs_vert @djunct_is_label.py @djunct_json_value.py
@djunct_make_script_and_rst.py @djunct_modal_smoothing_with_rep @djunct_montage_coordinator @djunct_overlap_check
@djunct_select_str.py @djunct_slice_space @djunct_ssw_intermed_edge_imgs @djunct_vol_3slice_select
@DO.examples @DoPerRoi.py DoPerRoi.py DriveSuma
dsetstat2p DTIStudioFibertoSegments @DTI_studio_reposition eg_main_chrono.py
@ElectroGrid ent16 a epi_b0_correct.py @ExamineGenFeatDists
ExamineXmat @extract_meica_ortvec @fast_roi FATCAT_matplot
fat_lat_csv.py fat_mat2d_plot.py fat_mat_sel.py fat_mat_tableize.py
fat_mvm_gridconv.py fat_mvm_prep.py fat_mvm_review.py fat_mvm_scripter.py
fat_proc_align_anat_pair fat_proc_axialize_anat fat_proc_connec_vis fat_proc_convert_dcm_anat
fat_proc_convert_dcm_dwis fat_proc_decmap fat_proc_dwi_to_dt fat_proc_filter_dwis
fat_proc_grad_plot fat_proc_imit2w_from_t1w fat_proc_map_to_dti fat_proc_select_vols
fat_roi_row.py @fat_tract_colorize fdrval file_tool
FIRdesign @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 gen_ss_review_table.py
@GetAfniBin @GetAfniDims @GetAfniID get_afni_model_PRF
get_afni_model_PRF_6 get_afni_model_PRF_6_BAD @GetAfniOrient @GetAfniPrefix
@GetAfniRes @get.afni.version @GetAfniView gifti_tool
@global_parse GLTsymtest @GradFlipTest @grayplot
HalloSuma @help.AFNI Ifile a im2niml a
images_equal imand a imaver a imcalc a
imcat a imcutup a imdump a immask a
imreg a imrotate a imstack a imstat a
imupsam a inspec @Install_3dPFM_Demo @Install_AfniRetinoDemo
@Install_AP_MULTI_DEMO1 @Install_APMULTI_Demo1_rest @Install_ClustScat_Demo @Install_D99_macaque
@Install_DBSproc @Install_FATCAT_DEMO @Install_FATCAT_DEMO2 @Install_FATMVM_DEMO
@Install_IBT_DATASETS @Install_InstaCorr_Demo @Install_MACAQUE_DEMO @Install_MACAQUE_DEMO_REST
@Install_MEICA_Demo @Install_NIH_Marmoset @Install_NMT @Install_RSFMRI_Motion_Group_Demo
@Install_SURFLAYERS_DEMO1 @Install_TSrestMovieDemo InstaTract @isOblique
@IsoMasks IsoSurface lesion_align MakeColorMap
@MakeLabelTable make_latest_tgz.csh @make_plug_diff make_pq_script.py
make_random_timing.py @make_stim_file make_stim_times.py MapIcosahedron
map_TrackID mayo_analyze a MBA @measure_bb_thick
@measure_erosion_thick @measure_in2out meica.py @move.to.series.dirs
mritopgm a mycat neuro_deconvolve.py nifti1_test
nifti1_tool nifti_tool niml_feedme niprobe
@NoExt @NoisySkullStrip @NoPound @np
nsize a p2dsetstat @parse_afni_name parse_fs_lt_log.py
@parse_name ParseName plugout_drive plugout_ijk
plugout_tt prompt_popup prompt_user PTA
@Purify_1D python_module_test.py quick.alpha.vals.py quickspec
quickspecSL @Quiet_Talkers quotize @radial_correlate
RBA read_matlab_files.py realtime_receiver.py @RenamePanga a
@Reorder @RetinoProc RetroTS.py @R_funclist
ROI2dataset @ROI_Corr_Mat @ROI_decluster ROIgrow
@ROI_modal_grow rotcom rPkgsInstall RSFgen
rtfeedme SampBias ScaleToMap @ScaleVolume
@ScriptCheck serial_helper @Shift_Volume @ShowDynamicRange
siemens_vision a @simulate_motion @SkullStrip_TouchUp slow_surf_clustsim.py
@snapshot_volreg @snapshot_volreg3 SpharmDeco @Spharm.examples
SpharmReco sqwave a @SSwarper stimband
strblast a suma @suma_acknowledge @SUMA_AlignToExperiment
suma_change_spec @SUMA_FSvolToBRIK @SUMA_Make_Spec_Caret @SUMA_Make_Spec_FS
@SUMA_Make_Spec_SF @SUMA_renumber_FS @suma_reprefixize_spec Surf2VolCoord
SurfaceMetrics SurfClust SurfDist SurfDsetInfo
SurfExtrema SurfFWHM SurfInfo SurfLayers
SurfLocalstat SurfMeasures SurfMesh SurfPatch
SurfQual SurfRetinoMap SurfSmooth @SurfSmooth.HEAT_07.examples
SurfToSurf @surf_to_vol_spackle @T1scale tedana_wrapper.py
@thickness_master @TimeDiff timing_tool.py to3d
tokens @toMNI_Awarp @toMNI_Qwarpar @ToRAI
TRR uber_align_test.py uber_skel.py uber_subject.py
uber_ttest.py uniq_images unWarpEPI.py @update.afni.binaries
Vecwarp @VolCenter waver a whereami
whirlgif xmat_tool.py Xphace a @xyz_to_ijk
README.3dsvm.realtime README.afnigui README.atlas_building README.attributes
README.bzip2 README.caez_atlas_build 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.texlike README.volreg README.web
README.ziad AFNI.changes.dglen AFNI.changes.rickr AFNI.afnirc
AFNI.Xdefaults

This page auto-generated on Tue Jan 18 13:42:19 EST 2022 — RWCox