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AFNI, SUMA and FATCAT: v16.0.11 (doc v2.1)
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7. Each program’s “Help”
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7.1. Help output of AFNI programs
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7.1.419. fat_mvm_review.py
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Table Of Contents
1. Installation and Background
2. SUMA
3. FATCAT
4. Statistics
5. Tutorials, Demos
6. Demo Material
7. Each program’s “Help”
7.1. Help output of AFNI programs
7.1.1. 1dAstrip
7.1.2. 1dBandpass
7.1.3. 1dBport
7.1.4. 1dCorrelate
7.1.5. 1dDW_Grad_o_Mat
7.1.6. 1dFlagMotion
7.1.7. 1dMarry
7.1.8. 1dNLfit
7.1.9. 1dRplot
7.1.10. 1dSEM
7.1.11. 1dTsort
7.1.12. 1dUpsample
7.1.13. 1d_tool.py
7.1.14. 1dcat
7.1.15. 1ddot
7.1.16. 1deval
7.1.17. 1dfft
7.1.18. 1dgenARMA11
7.1.19. 1dgrayplot
7.1.20. 1dmatcalc
7.1.21. 1dnorm
7.1.22. 1dplot
7.1.23. 1dsum
7.1.24. 1dsvd
7.1.25. 1dtranspose
7.1.26. 24swap
7.1.27. 2dImReg
7.1.28. 2perm
7.1.29. 2swap
7.1.30. 3dABoverlap
7.1.31. 3dAFNIto3D
7.1.32. 3dAFNItoANALYZE
7.1.33. 3dAFNItoMINC
7.1.34. 3dAFNItoNIFTI
7.1.35. 3dAFNItoNIML
7.1.36. 3dAFNItoRaw
7.1.37. 3dANALYZEtoAFNI
7.1.38. 3dANOVA
7.1.39. 3dANOVA2
7.1.40. 3dANOVA3
7.1.41. 3dAcost
7.1.42. 3dAllineate
7.1.43. 3dAnatNudge
7.1.44. 3dAnhist
7.1.45. 3dAttribute
7.1.46. 3dAutoTcorrelate
7.1.47. 3dAutobox
7.1.48. 3dAutomask
7.1.49. 3dBRAIN_VOYAGERtoAFNI
7.1.50. 3dBandpass
7.1.51. 3dBlurInMask
7.1.52. 3dBlurToFWHM
7.1.53. 3dBrickStat
7.1.54. 3dCM
7.1.55. 3dCRUISEtoAFNI
7.1.56. 3dClipLevel
7.1.57. 3dClustCount
7.1.58. 3dClustSim
7.1.59. 3dConformist
7.1.60. 3dConvolve
7.1.61. 3dCountSpikes
7.1.62. 3dDFT
7.1.63. 3dDTeig
7.1.64. 3dDTtoDWI
7.1.65. 3dDTtoNoisyDWI
7.1.66. 3dDWItoDT
7.1.67. 3dDWUncert
7.1.68. 3dDeconvolve
7.1.69. 3dDeconvolve_f
7.1.70. 3dDespike
7.1.71. 3dDetrend
7.1.72. 3dEigsToDT
7.1.73. 3dEmpty
7.1.74. 3dEntropy
7.1.75. 3dErrtsCormat
7.1.76. 3dExtrema
7.1.77. 3dFDR
7.1.78. 3dFFT
7.1.79. 3dFWHM
7.1.80. 3dFWHMx
7.1.81. 3dFourier
7.1.82. 3dFriedman
7.1.83. 3dGenFeatureDist
7.1.84. 3dGenPriors
7.1.85. 3dGetrow
7.1.86. 3dGroupInCorr
7.1.87. 3dHist
7.1.88. 3dIntracranial
7.1.89. 3dInvFMRI
7.1.90. 3dKruskalWallis
7.1.91. 3dLME
7.1.92. 3dLRflip
7.1.93. 3dLSS
7.1.94. 3dLocalBistat
7.1.95. 3dLocalHistog
7.1.96. 3dLocalPV
7.1.97. 3dLocalSVD
7.1.98. 3dLocalstat
7.1.99. 3dMEMA
7.1.100. 3dMINCtoAFNI
7.1.101. 3dMVM
7.1.102. 3dMannWhitney
7.1.103. 3dMaskToASCII
7.1.104. 3dMatch
7.1.105. 3dMax
7.1.106. 3dMean
7.1.107. 3dMedianFilter
7.1.108. 3dNLfim
7.1.109. 3dNetCorr
7.1.110. 3dNormalityTest
7.1.111. 3dNotes
7.1.112. 3dNwarpAdjust
7.1.113. 3dNwarpApply
7.1.114. 3dNwarpCalc
7.1.115. 3dNwarpCat
7.1.116. 3dNwarpFuncs
7.1.117. 3dNwarpXYZ
7.1.118. 3dOverlap
7.1.119. 3dPAR2AFNI.pl
7.1.120. 3dPFM
7.1.121. 3dPeriodogram
7.1.122. 3dPolyfit
7.1.123. 3dProbTrackID
7.1.124. 3dPval
7.1.125. 3dQwarp
7.1.126. 3dREMLfit
7.1.127. 3dROIMaker
7.1.128. 3dROIstats
7.1.129. 3dRSFC
7.1.130. 3dRank
7.1.131. 3dRankizer
7.1.132. 3dReHo
7.1.133. 3dRegAna
7.1.134. 3dRetinoPhase
7.1.135. 3dRowFillin
7.1.136. 3dRprogDemo
7.1.137. 3dSeg
7.1.138. 3dSetupGroupInCorr
7.1.139. 3dSignatures
7.1.140. 3dSkullStrip
7.1.141. 3dSpatNorm
7.1.142. 3dStatClust
7.1.143. 3dSurf2Vol
7.1.144. 3dSurfMask
7.1.145. 3dSynthesize
7.1.146. 3dTORTOISEtoHere
7.1.147. 3dTRfix
7.1.148. 3dTSgen
7.1.149. 3dTagalign
7.1.150. 3dTcat
7.1.151. 3dTcorr1D
7.1.152. 3dTcorrMap
7.1.153. 3dTcorrelate
7.1.154. 3dTfitter
7.1.155. 3dThreetoRGB
7.1.156. 3dTnorm
7.1.157. 3dToutcount
7.1.158. 3dToyProg
7.1.159. 3dTproject
7.1.160. 3dTqual
7.1.161. 3dTrackID
7.1.162. 3dTshift
7.1.163. 3dTsmooth
7.1.164. 3dTsort
7.1.165. 3dTstat
7.1.166. 3dTwotoComplex
7.1.167. 3dUndump
7.1.168. 3dUnifize
7.1.169. 3dUniformize
7.1.170. 3dUpsample
7.1.171. 3dVecRGB_to_HSL
7.1.172. 3dVol2Surf
7.1.173. 3dWarp
7.1.174. 3dWarpDrive
7.1.175. 3dWavelets
7.1.176. 3dWilcoxon
7.1.177. 3dWinsor
7.1.178. 3dXYZcat
7.1.179. 3dZcat
7.1.180. 3dZcutup
7.1.181. 3dZeropad
7.1.182. 3dZregrid
7.1.183. 3danisosmooth
7.1.184. 3daxialize
7.1.185. 3dbuc2fim
7.1.186. 3dbucket
7.1.187. 3dcalc
7.1.188. 3dclust
7.1.189. 3dcopy
7.1.190. 3ddelay
7.1.191. 3ddot
7.1.192. 3ddot_beta
7.1.193. 3ddup
7.1.194. 3dedge3
7.1.195. 3dfim
7.1.196. 3dfim+
7.1.197. 3dfractionize
7.1.198. 3dhistog
7.1.199. 3dinfill
7.1.200. 3dinfo
7.1.201. 3dkmeans
7.1.202. 3dmaskSVD
7.1.203. 3dmask_tool
7.1.204. 3dmaskave
7.1.205. 3dmaskdump
7.1.206. 3dmatcalc
7.1.207. 3dmatmult
7.1.208. 3dmaxima
7.1.209. 3dmerge
7.1.210. 3dnewid
7.1.211. 3dnoise
7.1.212. 3dnvals
7.1.213. 3dpc
7.1.214. 3dproject
7.1.215. 3drefit
7.1.216. 3drename
7.1.217. 3dresample
7.1.218. 3dretroicor
7.1.219. 3drotate
7.1.220. 3dsvm
7.1.221. 3dttest
7.1.222. 3dttest++
7.1.223. 3dvolreg
7.1.224. 4swap
7.1.225. @1dDiffMag
7.1.226. @2dwarper
7.1.227. @2dwarper.Allin
7.1.228. @4Daverage
7.1.229. @ANATICOR
7.1.230. @AddEdge
7.1.231. @AfniEnv
7.1.232. @AfniOrient2RAImap
7.1.233. @AfniOrientSign
7.1.234. @Align_Centers
7.1.235. @Atlasize
7.1.236. @Center_Distance
7.1.237. @CheckForAfniDset
7.1.238. @CommandGlobb
7.1.239. @DO.examples
7.1.240. @DTI_studio_reposition
7.1.241. @DeblankFileNames
7.1.242. @DiceMetric
7.1.243. @DoPerRoi.py
7.1.244. @DriveAfni
7.1.245. @DriveSuma
7.1.246. @ElectroGrid
7.1.247. @ExamineGenFeatDists
7.1.248. @FS_roi_label
7.1.249. @FSlabel2dset
7.1.250. @FindAfniDsetPath
7.1.251. @FromRAI
7.1.252. @FullPath
7.1.253. @GetAfniBin
7.1.254. @GetAfniDims
7.1.255. @GetAfniID
7.1.256. @GetAfniOrient
7.1.257. @GetAfniPrefix
7.1.258. @GetAfniRes
7.1.259. @GetAfniView
7.1.260. @GradFlipTest
7.1.261. @Install_3dPFM_Demo
7.1.262. @Install_AfniRetinoDemo
7.1.263. @Install_ClustScat_Demo
7.1.264. @Install_DBSproc
7.1.265. @Install_FATCAT_DEMO
7.1.266. @Install_FATMVM_DEMO
7.1.267. @Install_InstaCorr_Demo
7.1.268. @Install_MEICA_Demo
7.1.269. @Install_RSFMRI_Motion_Group_Demo
7.1.270. @Install_TSrestMovieDemo
7.1.271. @IsoMasks
7.1.272. @MakeLabelTable
7.1.273. @NoExt
7.1.274. @NoPound
7.1.275. @NoisySkullStrip
7.1.276. @Purify_1D
7.1.277. @Quiet_Talkers
7.1.278. @ROI_Corr_Mat
7.1.279. @R_funclist
7.1.280. @RenamePanga
7.1.281. @Reorder
7.1.282. @RetinoProc
7.1.283. @SUMA_AlignToExperiment
7.1.284. @SUMA_FSvolToBRIK
7.1.285. @SUMA_Make_Spec_Caret
7.1.286. @SUMA_Make_Spec_FS
7.1.287. @SUMA_Make_Spec_SF
7.1.288. @ScaleVolume
7.1.289. @ScriptCheck
7.1.290. @Shift_Volume
7.1.291. @ShowDynamicRange
7.1.292. @Spharm.examples
7.1.293. @SurfSmooth.HEAT_07.examples
7.1.294. @T1scale
7.1.295. @TimeDiff
7.1.296. @ToRAI
7.1.297. @UpdateAfni
7.1.298. @VolCenter
7.1.299. @afni.run.me
7.1.300. @align_partial_oblique
7.1.301. @auto_align
7.1.302. @auto_tlrc
7.1.303. @build_afni_Xlib
7.1.304. @clean_help_dir
7.1.305. @clip_volume
7.1.306. @compute_gcor
7.1.307. @demo_prompt
7.1.308. @diff.files
7.1.309. @diff.tree
7.1.310. @escape-
7.1.311. @fast_roi
7.1.312. @fix_FSsphere
7.1.313. @float_fix
7.1.314. @get.afni.version
7.1.315. @global_parse
7.1.316. @help.AFNI
7.1.317. @isOblique
7.1.318. @make_plug_diff
7.1.319. @make_stim_file
7.1.320. @move.to.series.dirs
7.1.321. @np
7.1.322. @parse_afni_name
7.1.323. @parse_name
7.1.324. @radial_correlate
7.1.325. @simulate_motion
7.1.326. @statauxcode
7.1.327. @toMNI_Awarp
7.1.328. @toMNI_Qwarpar
7.1.329. @update.afni.binaries
7.1.330. AFNI_Batch_R
7.1.331. AlphaSim
7.1.332. AnalyzeTrace
7.1.333. BrainSkin
7.1.334. CompareSurfaces
7.1.335. ConvertDset
7.1.336. ConvertSurface
7.1.337. ConvexHull
7.1.338. CreateIcosahedron
7.1.339. DTIStudioFibertoSegments
7.1.340. Dimon
7.1.341. Dimon1
7.1.342. DriveSuma
7.1.343. ExamineXmat
7.1.344. FD2
7.1.345. FIRdesign
7.1.346. FSread_annot
7.1.347. GLTsymtest
7.1.348. HalloSuma
7.1.349. Ifile
7.1.350. InstaTract
7.1.351. IsoSurface
7.1.352. MakeColorMap
7.1.353. MapIcosahedron
7.1.354. ParseName
7.1.355. ROI2dataset
7.1.356. ROIgrow
7.1.357. RSFgen
7.1.358. SUMA_glxdino
7.1.359. SUMA_paperplane
7.1.360. SUMA_pixmap2eps
7.1.361. SampBias
7.1.362. ScaleToMap
7.1.363. SpharmDeco
7.1.364. SpharmReco
7.1.365. Surf2VolCoord
7.1.366. SurfClust
7.1.367. SurfDist
7.1.368. SurfDsetInfo
7.1.369. SurfExtrema
7.1.370. SurfFWHM
7.1.371. SurfInfo
7.1.372. SurfMeasures
7.1.373. SurfMesh
7.1.374. SurfPatch
7.1.375. SurfQual
7.1.376. SurfRetinoMap
7.1.377. SurfSmooth
7.1.378. SurfToSurf
7.1.379. SurfaceMetrics
7.1.380. Vecwarp
7.1.381. Xphace
7.1.382. abut
7.1.383. adwarp
7.1.384. afni
7.1.385. afni_history
7.1.386. afni_open
7.1.387. afni_proc.py
7.1.388. afni_restproc.py
7.1.389. afni_run_R
7.1.390. afni_skeleton.py
7.1.391. afni_system_check.py
7.1.392. afni_util.py
7.1.393. afni_vcheck
7.1.394. aiv
7.1.395. align_epi_anat.py
7.1.396. apsearch
7.1.397. auto_warp.py
7.1.398. balloon
7.1.399. byteorder
7.1.400. cat_matvec
7.1.401. ccalc
7.1.402. cdf
7.1.403. cifti_tool
7.1.404. cjpeg
7.1.405. column_cat
7.1.406. count
7.1.407. demo.fixed.niml.do
7.1.408. demo.mobile.niml.do
7.1.409. dicom_hdr
7.1.410. dicom_hinfo
7.1.411. dicom_to_raw
7.1.412. djpeg
7.1.413. eg_main_chrono.py
7.1.414. ent16
7.1.415. fat_lat_csv.py
7.1.416. fat_mat_sel.py
7.1.417. fat_mvm_gridconv.py
7.1.418. fat_mvm_prep.py
7.1.419. fat_mvm_review.py
7.1.420. fat_mvm_scripter.py
7.1.421. fat_roi_row.py
7.1.422. fdrval
7.1.423. fftest
7.1.424. file_tool
7.1.425. fim2
7.1.426. float_scan
7.1.427. from3d
7.1.428. ftosh
7.1.429. ge_header
7.1.430. gen_epi_review.py
7.1.431. gen_group_command.py
7.1.432. gen_ss_review_scripts.py
7.1.433. gen_ss_review_table.py
7.1.434. gifti_tool
7.1.435. help_format
7.1.436. im2niml
7.1.437. images_equal
7.1.438. imand
7.1.439. imaver
7.1.440. imcalc
7.1.441. imcat
7.1.442. imcutup
7.1.443. imdump
7.1.444. immask
7.1.445. imreg
7.1.446. imrotate
7.1.447. imstack
7.1.448. imstat
7.1.449. imupsam
7.1.450. inspec
7.1.451. lpc_align.py
7.1.452. make_pq_script.py
7.1.453. make_random_timing.py
7.1.454. make_stim_times.py
7.1.455. map_TrackID
7.1.456. mayo_analyze
7.1.457. meica.py
7.1.458. mpeg_encode
7.1.459. mritopgm
7.1.460. mycat
7.1.461. myget
7.1.462. neuro_deconvolve.py
7.1.463. nicat
7.1.464. niccc
7.1.465. nifti1_test
7.1.466. nifti1_tool
7.1.467. nifti_tool
7.1.468. niml_feedme
7.1.469. niprobe
7.1.470. nsize
7.1.471. plugout_drive
7.1.472. plugout_ijk
7.1.473. plugout_tt
7.1.474. plugout_tta
7.1.475. prompt_user
7.1.476. python_module_test.py
7.1.477. qdelaunay
7.1.478. qhull
7.1.479. quick.alpha.vals.py
7.1.480. quickspec
7.1.481. quotize
7.1.482. rPkgsInstall
7.1.483. rbox
7.1.484. read_matlab_files.py
7.1.485. realtime_receiver.py
7.1.486. rmz
7.1.487. rotcom
7.1.488. rtfeedme
7.1.489. serial_helper
7.1.490. sfim
7.1.491. siemens_vision
7.1.492. slow_surf_clustsim.py
7.1.493. sqwave
7.1.494. stimband
7.1.495. strblast
7.1.496. suma
7.1.497. suma_change_spec
7.1.498. tfim
7.1.499. timing_tool.py
7.1.500. to3d
7.1.501. tokens
7.1.502. uber_align_test.py
7.1.503. uber_proc.py
7.1.504. uber_skel.py
7.1.505. uber_subject.py
7.1.506. uber_ttest.py
7.1.507. uniq_images
7.1.508. waver
7.1.509. whereami
7.1.510. whirlgif
7.1.511. xmat_tool.py
8. Glossary
9. References
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