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++
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
3dAFNItoNIFTI	3dAFNItoNIML	3dAFNItoRaw
3dANOVA	3dANOVA2	3dANOVA3
3dAcost	3dAllineate	3dAmpToRSFC
3dAnhist	3dAttribute	3dAutoTcorrelate
3dAutobox	3dAutomask	3dBRAIN_VOYAGERtoAFNI
3dBallMatch	3dBandpass	3dBlurInMask
3dBlurToFWHM	3dBrainSync	3dBrickStat
3dCM	3dCRUISEtoAFNI	3dClipLevel
3dClustCount	3dClustSim	3dClusterize
3dCompareAffine	3dConformist	3dConvolve
3dDFT	3dDTeig	3dDTtoDWI
3dDTtoNoisyDWI	3dDWItoDT	3dDWUncert
3dDeconvolve	3dDegreeCentrality	3dDepthMap
3dDespike	3dDetrend	3dDiff
3dECM	3dEdu_01_scale	3dEigsToDT
3dEmpty	3dEntropy	3dErrtsCormat
3dExchange	3dExtractGroupInCorr	3dExtrema
3dFDR	3dFFT	3dFWHMx
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	3dMSE	3dMSS
3dMVM	3dMVM_validator	3dMannWhitney
3dMaskToASCII	3dMatch	3dMean
3dMedianFilter	3dMultiThresh	3dNLfim
3dNetCorr	3dNormalityTest	3dNotes
3dNwarpAdjust	3dNwarpApply	3dNwarpCalc
3dNwarpCat	3dNwarpFuncs	3dNwarpXYZ
3dOverlap	3dPAR2AFNI.pl	3dPFM
3dPVmap	3dPeriodogram	3dPolyfit
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
3dUpsample	3dVecRGB_to_HSL	3dVol2Surf
3dWarp	3dWarpDrive	3dWilcoxon
3dWinsor	3dXClustSim	3dXYZcat
3dZcat	3dZcutup	3dZeropad
3dZipperZapper	3dZregrid	3danisosmooth
3daxialize	3dbucket	3dcalc
3dclust	3dcopy	3ddelay
3ddot	3ddot_beta	3dedge3
3dedgedog	3dfim+	3dfractionize
3dhistog	3dinfill	3dinfo
3dkmeans	3dmaskSVD	3dmask_tool
3dmaskave	3dmaskdump	3dmatcalc
3dmatmult	3dmaxdisp	3dmaxima
3dmerge	3dnewid	3dnvals
3dpc	3drefit	3drename
3dresample	3dretroicor	3drotate
3dsvm	3dsvm_linpredict	3dtoXdataset
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	@DeblankFileNames
@DiceMetric	@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_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
@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_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_dwi_selector.tcsh	@djunct_edgy_align_check
@djunct_glue_imgs_vert	@djunct_json_value.py	@djunct_modal_smoothing_with_rep
@djunct_montage_coordinator	@djunct_overlap_check	@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	@measure_bb_thick
@measure_erosion_thick	@measure_in2out	@move.to.series.dirs
@np	@parse_afni_name	@parse_name
@radial_correlate	@simulate_motion	@snapshot_volreg
@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	AnalyzeTrace	BayesianGroupAna.py
BrainSkin	ClustExp_HistTable.py	ClustExp_StatParse.py
CompareSurfaces	ConvertDset	ConvertSurface
ConvexHull	CreateIcosahedron	DTIStudioFibertoSegments
Dimon	DriveSuma	ExamineXmat
FATCAT_matplot	FIRdesign	FSread_annot
GLTsymtest	HalloSuma	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	abids_json_info.py	abids_json_tool.py
abids_tool.py	adjunct_apqc_tsnr_general	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_roi_info	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_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
cifti_tool	cjpeg	column_cat
compute_ROI_stats.tcsh	convert_cdiflist_to_grads.py	count
count_afni	dcm2niix_afni	desphinxify
dicom_hdr	dicom_hinfo	dicom_to_raw
djpeg	dsetstat2p	eg_main_chrono.py
epi_b0_correct.py	fat_mat2d_plot.py	fat_mat_sel.py
fat_mat_tableize.py	fat_mvm_gridconv.py	fat_mvm_prep.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_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	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
gtkyd_check.py	help_format	im2niml
images_equal	imand	imaver
imcalc	imcat	imcutup
imdump	immask	imreg
imrotate	imstack	imstat
imupsam	init_user_dotfiles.py	inspec
lesion_align	make_pq_script.py	make_random_timing.py
make_stim_times.py	map_TrackID	map_ap_to_deriv.py
meica.py	mycat	myget
neuro_deconvolve.py	nicat	niccc
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
slow_surf_clustsim.py	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
whereami_afni	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