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 3dLME2 3dLMEr
3dLocalACF 3dLocalBistat 3dLocalHistog 3dLocalPV
3dLocalstat 3dLocalSVD 3dLocalUnifize 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_atlas_points_to_labeltable adjunct_aw_tableize_roi_info.py adjunct_calc_mont_dims.py
adjunct_combine_str.py adjunct_deob_around_origin adjunct_is_label.py adjunct_make_script_and_rst.py
adjunct_middle_pair_mask 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_me.tcsh ap_run_simple_rest.tcsh
apsearch @Atlasize @auto_tlrc auto_warp.py
balloon BayesianGroupAna.py bayes_view BrainSkin
build_afni.py @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
compute_ROI_stats.tcsh 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 find_variance_lines.tcsh FIRdesign @fix_FSsphere
@float_fix float_scan from3d a @FromRAI
@FSlabel2dset FSread_annot @FS_roi_label ftosh a
@FullPath ge_header a gen_cluster_table 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 gtkyd_check
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 index.html.2023_06_26_1618 index.html.2023_10_02_1534 init_user_dotfiles.py
inspec @Install_3dPFM_Demo @Install_AfniRetinoDemo @Install_AP_MULTI_DEMO1
@Install_APMULTI_Demo1_rest @Install_APMULTI_Demo2_realtime @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_MBM_Marmoset @Install_MEICA_Demo @Install_NIH_Marmoset @Install_NMT
@Install_RAT_DEMO_REST @Install_RSFMRI_Motion_Group_Demo @Install_SAM_marmoset @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
open_apqc.py p2dsetstat @parse_afni_name parse_fs_lt_log.py
@parse_name ParseName physio_calc.py 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 roi_stats_warnings.py 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 sswarper2 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 test_afni_prog_help.tcsh
@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 Apr 23 20:38:00 EDT 2024 — RWCox