4.1. Alphabetical list of program helps

4.1.1. 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 HERE, where programs are loosely grouped by topic and functionality, with a brief description of each provided.

1dApar2mat	1dAstrip	1dBandpass
1dBport	1dCorrelate	1dDW_Grad_o_Mat
1dDW_Grad_o_Mat++	1dFlagMotion	1dMarry
1dNLfit	1dRplot	1dSEM
1dTsort	1dUpsample	1d_tool.py
1dcat	1ddot	1deval
1dfft	1dgenARMA11	1dgrayplot
1dmatcalc	1dnorm	1dplot
1dplot.py	1dsound	1dsum
1dsvd	1dtranspose	24swap
2dImReg	2dcat	2perm
2swap	3dABoverlap	3dAFNIto3D
3dAFNItoANALYZE	3dAFNItoMINC	3dAFNItoNIFTI
3dAFNItoNIML	3dAFNItoRaw	3dANALYZEtoAFNI
3dANOVA	3dANOVA2	3dANOVA3
3dAcost	3dAllineate	3dAmpToRSFC
3dAnatNudge	3dAnhist	3dAttribute
3dAutoTcorrelate	3dAutobox	3dAutomask
3dBRAIN_VOYAGERtoAFNI	3dBallMatch	3dBandpass
3dBlurInMask	3dBlurToFWHM	3dBrainSync
3dBrickStat	3dCM	3dCRUISEtoAFNI
3dClipLevel	3dClustCount	3dClustSim
3dClusterize	3dCompareAffine	3dConformist
3dConvolve	3dCountSpikes	3dDFT
3dDTeig	3dDTtoDWI	3dDTtoNoisyDWI
3dDWItoDT	3dDWUncert	3dDeconvolve
3dDeconvolve_f	3dDegreeCentrality	3dDepthMap
3dDespike	3dDetrend	3dDiff
3dECM	3dEduProg	3dEdu_01_scale
3dEigsToDT	3dEmpty	3dEntropy
3dErrtsCormat	3dEulerDist	3dExchange
3dExtractGroupInCorr	3dExtrema	3dFDR
3dFFT	3dFWHM	3dFWHMx
3dFourier	3dFriedman	3dGenFeatureDist
3dGenPriors	3dGetrow	3dGrayplot
3dGroupInCorr	3dHist	3dICC
3dISC	3dIntracranial	3dInvFMRI
3dKruskalWallis	3dLFCD	3dLME
3dLME2	3dLMEr	3dLRflip
3dLSS	3dLocalACF	3dLocalBistat
3dLocalHistog	3dLocalPV	3dLocalSVD
3dLocalUnifize	3dLocalstat	3dLombScargle
3dMEMA	3dMEPFM	3dMINCtoAFNI
3dMSE	3dMSS	3dMVM
3dMVM_validator	3dMannWhitney	3dMaskToASCII
3dMatch	3dMax	3dMean
3dMedianFilter	3dMultiThresh	3dNLfim
3dNetCorr	3dNormalityTest	3dNotes
3dNwarpAdjust	3dNwarpApply	3dNwarpCalc
3dNwarpCat	3dNwarpFuncs	3dNwarpXYZ
3dOverlap	3dPAR2AFNI.pl	3dPFM
3dPVmap	3dPeriodogram	3dPolyfit
3dProbTrackID	3dPval	3dQwarp
3dREMLfit	3dROIMaker	3dROIstats
3dRSFC	3dRank	3dRankizer
3dReHo	3dRegAna	3dRetinoPhase
3dRowFillin	3dRprogDemo	3dSeg
3dSetupGroupInCorr	3dSharpen	3dSignatures
3dSkullStrip	3dSliceNDice	3dSpaceTimeCorr
3dSpatNorm	3dStatClust	3dSurf2Vol
3dSurfMask	3dSynthesize	3dTORTOISEtoHere
3dTRfix	3dTSgen	3dTagalign
3dTcat	3dTcorr1D	3dTcorrMap
3dTcorrelate	3dTfilter	3dTfitter
3dThreetoRGB	3dTnorm	3dToutcount
3dToyProg	3dTproject	3dTqual
3dTrackID	3dTshift	3dTsmooth
3dTsort	3dTsplit4D	3dTstat
3dTto1D	3dTwotoComplex	3dUndump
3dUnifize	3dUniformize	3dUpsample
3dVecRGB_to_HSL	3dVol2Surf	3dWarp
3dWarpDrive	3dWavelets	3dWilcoxon
3dWinsor	3dXClustSim	3dXYZcat
3dZcat	3dZcutup	3dZeropad
3dZipperZapper	3dZregrid	3danisosmooth
3daxialize	3dbuc2fim	3dbucket
3dcalc	3dclust	3dcopy
3ddelay	3ddot	3ddot_beta
3ddup	3dedge3	3dedgedog
3dfim	3dfim+	3dfractionize
3dhistog	3dinfill	3dinfo
3dkmeans	3dmaskSVD	3dmask_tool
3dmaskave	3dmaskdump	3dmatcalc
3dmatmult	3dmaxdisp	3dmaxima
3dmerge	3dnewid	3dnoise
3dnvals	3dpc	3dproject
3drefit	3drename	3dresample
3dretroicor	3drotate	3dsvm
3dsvm_linpredict	3dtoXdataset	3dttest
3dttest++	3dvolreg	4swap
@1dDiffMag	@2dwarper	@2dwarper.Allin
@4Daverage	@ANATICOR	@AddEdge
@AfniEnv	@AfniOrient2RAImap	@AfniOrientSign
@Align_Centers	@Atlasize	@Center_Distance
@CheckForAfniDset	@ClustExp_CatLab	@ClustExp_run_shiny
@CommandGlobb	@DO.examples	@DTI_studio_reposition
@DeblankFileNames	@DiceMetric	@DoPerRoi.py
@DriveAfni	@DriveSuma	@ElectroGrid
@ExamineGenFeatDists	@FS_roi_label	@FSlabel2dset
@FindAfniDsetPath	@FromRAI	@FullPath
@GetAfniBin	@GetAfniDims	@GetAfniID
@GetAfniOrient	@GetAfniPrefix	@GetAfniRes
@GetAfniView	@GradFlipTest	@Install_3dPFM_Demo
@Install_APMULTI_Demo1_rest	@Install_APMULTI_Demo2_realtime	@Install_AP_MULTI_DEMO1
@Install_AfniRetinoDemo	@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	@IsoMasks
@MakeLabelTable	@NoExt	@NoPound
@NoisySkullStrip	@Purify_1D	@Quiet_Talkers
@ROI_Corr_Mat	@ROI_decluster	@ROI_modal_grow
@R_funclist	@RenamePanga	@Reorder
@RetinoProc	@SSwarper	@SUMA_AlignToExperiment
@SUMA_FSvolToBRIK	@SUMA_Make_Spec_Caret	@SUMA_Make_Spec_FS
@SUMA_Make_Spec_SF	@SUMA_renumber_FS	@ScaleVolume
@ScriptCheck	@Shift_Volume	@ShowDynamicRange
@SkullStrip_TouchUp	@Spharm.examples	@SurfSmooth.HEAT_07.examples
@T1scale	@TimeDiff	@ToRAI
@UpdateAfni	@VolCenter	@afni.run.me
@afni_R_package_install	@afni_refacer_make_master	@afni_refacer_make_master_addendum
@afni_refacer_make_onebigA12	@afni_refacer_run	@align_partial_oblique
@animal_warper	@auto_align	@auto_tlrc
@build_afni_Xlib	@chauffeur_afni	@clean_help_dir
@clip_volume	@compute_OC_weights	@compute_gcor
@demo_prompt	@diff.files	@diff.tree
@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
@escape-	@extract_meica_ortvec	@fast_roi
@fat_tract_colorize	@fix_FSsphere	@float_fix
@get.afni.version	@global_parse	@grayplot
@help.AFNI	@isOblique	@make_plug_diff
@make_stim_file	@measure_bb_thick	@measure_erosion_thick
@measure_in2out	@move.to.series.dirs	@np
@parse_afni_name	@parse_name	@radial_correlate
@simulate_motion	@snapshot_volreg	@snapshot_volreg3
@statauxcode	@suma_acknowledge	@suma_reprefixize_spec
@surf_to_vol_spackle	@thickness_master	@toMNI_Awarp
@toMNI_Qwarpar	@update.afni.binaries	@xyz_to_ijk
AFNI_Batch_R	AlphaSim	AnalyzeTrace
BayesianGroupAna.py	BrainSkin	CA_EZ_atlas.csh
ClustExp_HistTable.py	ClustExp_StatParse.py	CompareSurfaces
ConvertDset	ConvertSurface	ConvexHull
CreateIcosahedron	DTIStudioFibertoSegments	Dimon
Dimon1	DoPerRoi.py	DriveSuma
ExamineXmat	FATCAT_matplot	FD2
FIRdesign	FSread_annot	GLTsymtest
HalloSuma	Ifile	InstaTract
IsoSurface	MBA	MakeColorMap
MapIcosahedron	PTA	ParseName
RBA	ROI2dataset	ROIgrow
RSFgen	RetroTS.py	SUMA_glxdino
SUMA_paperplane	SUMA_pixmap2eps	SampBias
ScaleToMap	SpharmDeco	SpharmReco
Surf2VolCoord	SurfClust	SurfDist
SurfDsetInfo	SurfExtrema	SurfFWHM
SurfInfo	SurfLayers	SurfLocalstat
SurfMeasures	SurfMesh	SurfPatch
SurfQual	SurfRetinoMap	SurfSmooth
SurfToSurf	SurfaceMetrics	TRR
Vecwarp	Xphace	abids_json_info.py
abids_json_tool.py	abids_tool.py	abut
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	afni_history	afni_open
afni_proc.py	afni_python_wrapper.py	afni_restproc.py
afni_run_R	afni_skeleton.py	afni_system_check.py
afni_vcheck	aiv	align_epi_anat.py
ap_run_simple_rest.tcsh	ap_run_simple_rest_me.tcsh	apqc_make_html.py
apqc_make_tcsh.py	apsearch	auto_warp.py
balloon	bayes_view	build_afni.py
byteorder	cat_matvec	ccalc
cdf	check_dset_for_fs.py	cifti_tool
cjpeg	column_cat	compute_ROI_stats.tcsh
convert_cdiflist_to_grads.py	count	dcm2niix_afni
demoExpt.py	dicom_hdr	dicom_hinfo
dicom_to_raw	djpeg	dsetstat2p
eg_main_chrono.py	ent16	epi_b0_correct.py
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
fdrval	fftest	file_tool
fim2	find_variance_lines.tcsh	float_scan
from3d	ftosh	ge_header
gen_cluster_table	gen_epi_review.py	gen_group_command.py
gen_ss_review_scripts.py	gen_ss_review_table.py	get_afni_model_PRF
get_afni_model_PRF_6	get_afni_model_PRF_6_BAD	gifti_tool
gtkyd_check	help_format	im2niml
images_equal	imand	imaver
imcalc	imcat	imcutup
imdump	immask	imreg
imrotate	imstack	imstat
imupsam	index.html.2023_06_26_1618	index.html.2023_10_02_1534
init_user_dotfiles.py	inspec	lesion_align
lpc_align.py	make_latest_tgz.csh	make_pq_script.py
make_random_timing.py	make_stim_times.py	map_TrackID
mayo_analyze	meica.py	mpeg_encode
mritopgm	mycat	myget
neuro_deconvolve.py	nicat	niccc
nifti1_test	nifti1_tool	nifti_tool
niml_feedme	niprobe	nsize
open_apqc.py	p2dsetstat	parse_fs_lt_log.py
physio_calc.py	plugout_drive	plugout_ijk
plugout_tt	plugout_tta	prompt_popup
prompt_user	python_module_test.py	quick.alpha.vals.py
quickspec	quickspecSL	quotize
rPkgsInstall	rbox	read_matlab_files.py
realtime_receiver.py	rmz	roi_stats_warnings.py
rotcom	rtfeedme	serial_helper
sfim	siemens_vision	slow_surf_clustsim.py
sqwave	sswarper2	stimband
strblast	suma	suma_change_spec
tedana_wrapper.py	test_afni_prog_help.tcsh	tfim
timing_tool.py	to3d	tokens
uber_align_test.py	uber_proc.py	uber_skel.py
uber_subject.py	uber_ttest.py	unWarpEPI.py
uniq_images	waver	whereami
whirlgif	xmat_tool.py

4.1.2. 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 HERE, contains information on such deprecations and pointers to the more modern version.

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