niwrap-afni 0.5.0__py3-none-any.whl

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  1. niwrap_afni/afni/__init__.py +582 -0
  2. niwrap_afni/afni/abids_json_info_py.py +247 -0
  3. niwrap_afni/afni/abids_json_tool_py.py +212 -0
  4. niwrap_afni/afni/abids_tool.py +191 -0
  5. niwrap_afni/afni/adjunct_apqc_tsnr_general.py +447 -0
  6. niwrap_afni/afni/adjunct_aw_tableize_roi_info_py.py +224 -0
  7. niwrap_afni/afni/adjunct_calc_mont_dims_py.py +173 -0
  8. niwrap_afni/afni/adjunct_combine_str_py.py +198 -0
  9. niwrap_afni/afni/adjunct_is_label_py.py +180 -0
  10. niwrap_afni/afni/adjunct_make_script_and_rst_py.py +237 -0
  11. niwrap_afni/afni/adjunct_select_str_py.py +188 -0
  12. niwrap_afni/afni/adjunct_simplify_cost.py +172 -0
  13. niwrap_afni/afni/adjunct_suma_fs_mask_and_qc.py +249 -0
  14. niwrap_afni/afni/adjunct_suma_fs_roi_info.py +228 -0
  15. niwrap_afni/afni/adjunct_tort_plot_dp_align.py +248 -0
  16. niwrap_afni/afni/adwarp.py +296 -0
  17. niwrap_afni/afni/afni.py +428 -0
  18. niwrap_afni/afni/afni_batch_r.py +215 -0
  19. niwrap_afni/afni/afni_check_omp.py +174 -0
  20. niwrap_afni/afni/afni_history.py +413 -0
  21. niwrap_afni/afni/afni_open.py +304 -0
  22. niwrap_afni/afni/afni_proc_py.py +283 -0
  23. niwrap_afni/afni/afni_run_r.py +180 -0
  24. niwrap_afni/afni/afni_system_check_py.py +274 -0
  25. niwrap_afni/afni/aiv.py +231 -0
  26. niwrap_afni/afni/align_epi_anat.py +356 -0
  27. niwrap_afni/afni/analyze_trace.py +292 -0
  28. niwrap_afni/afni/ap_run_simple_rest.py +293 -0
  29. niwrap_afni/afni/apqc_make_html.py +175 -0
  30. niwrap_afni/afni/apqc_make_tcsh_py.py +245 -0
  31. niwrap_afni/afni/apsearch.py +195 -0
  32. niwrap_afni/afni/auto_warp_py.py +527 -0
  33. niwrap_afni/afni/balloon.py +210 -0
  34. niwrap_afni/afni/bayes_view.py +196 -0
  35. niwrap_afni/afni/bayesian_group_ana_py.py +342 -0
  36. niwrap_afni/afni/brain_skin.py +358 -0
  37. niwrap_afni/afni/build_afni_py.py +330 -0
  38. niwrap_afni/afni/cat_matvec.py +185 -0
  39. niwrap_afni/afni/ccalc.py +192 -0
  40. niwrap_afni/afni/cifti_tool.py +271 -0
  41. niwrap_afni/afni/cjpeg.py +233 -0
  42. niwrap_afni/afni/clust_exp_hist_table_py.py +218 -0
  43. niwrap_afni/afni/clust_exp_stat_parse_py.py +346 -0
  44. niwrap_afni/afni/column_cat.py +208 -0
  45. niwrap_afni/afni/compare_surfaces.py +344 -0
  46. niwrap_afni/afni/convert_cdiflist_to_grads.py +251 -0
  47. niwrap_afni/afni/convert_dset.py +421 -0
  48. niwrap_afni/afni/convert_surface.py +247 -0
  49. niwrap_afni/afni/convex_hull.py +386 -0
  50. niwrap_afni/afni/count.py +327 -0
  51. niwrap_afni/afni/create_icosahedron.py +282 -0
  52. niwrap_afni/afni/dcm2niix_afni.py +550 -0
  53. niwrap_afni/afni/dicom_hdr.py +263 -0
  54. niwrap_afni/afni/dicom_hinfo.py +220 -0
  55. niwrap_afni/afni/dicom_to_raw.py +176 -0
  56. niwrap_afni/afni/dimon.py +286 -0
  57. niwrap_afni/afni/djpeg.py +233 -0
  58. niwrap_afni/afni/drive_suma.py +520 -0
  59. niwrap_afni/afni/dsetstat2p.py +218 -0
  60. niwrap_afni/afni/dtistudio_fiberto_segments.py +198 -0
  61. niwrap_afni/afni/epi_b0_correct.py +485 -0
  62. niwrap_afni/afni/examine_xmat.py +280 -0
  63. niwrap_afni/afni/fat_mat2d_plot_py.py +428 -0
  64. niwrap_afni/afni/fat_mat_sel_py.py +469 -0
  65. niwrap_afni/afni/fat_mat_tableize.py +292 -0
  66. niwrap_afni/afni/fat_mvm_gridconv_py.py +207 -0
  67. niwrap_afni/afni/fat_mvm_prep.py +256 -0
  68. niwrap_afni/afni/fat_mvm_scripter_py.py +353 -0
  69. niwrap_afni/afni/fat_proc_align_anat_pair.py +307 -0
  70. niwrap_afni/afni/fat_proc_axialize_anat.py +415 -0
  71. niwrap_afni/afni/fat_proc_connec_vis.py +346 -0
  72. niwrap_afni/afni/fat_proc_convert_dcm_anat.py +283 -0
  73. niwrap_afni/afni/fat_proc_convert_dcm_dwis.py +374 -0
  74. niwrap_afni/afni/fat_proc_decmap.py +321 -0
  75. niwrap_afni/afni/fat_proc_dwi_to_dt.py +522 -0
  76. niwrap_afni/afni/fat_proc_filter_dwis.py +321 -0
  77. niwrap_afni/afni/fat_proc_imit2w_from_t1w.py +283 -0
  78. niwrap_afni/afni/fat_proc_map_to_dti.py +308 -0
  79. niwrap_afni/afni/fat_proc_select_vols.py +266 -0
  80. niwrap_afni/afni/fat_roi_row.py +233 -0
  81. niwrap_afni/afni/fatcat_matplot.py +181 -0
  82. niwrap_afni/afni/fdrval.py +241 -0
  83. niwrap_afni/afni/fftest.py +197 -0
  84. niwrap_afni/afni/file_tool.py +580 -0
  85. niwrap_afni/afni/fim2.py +465 -0
  86. niwrap_afni/afni/find_variance_lines.py +353 -0
  87. niwrap_afni/afni/firdesign.py +235 -0
  88. niwrap_afni/afni/float_scan.py +213 -0
  89. niwrap_afni/afni/from3d.py +292 -0
  90. niwrap_afni/afni/fsread_annot.py +322 -0
  91. niwrap_afni/afni/gen_epi_review_py.py +292 -0
  92. niwrap_afni/afni/gen_group_command.py +324 -0
  93. niwrap_afni/afni/gen_ss_review_scripts.py +421 -0
  94. niwrap_afni/afni/gen_ss_review_table_py.py +324 -0
  95. niwrap_afni/afni/get_afni_model_prf.py +196 -0
  96. niwrap_afni/afni/get_afni_model_prf_6.py +222 -0
  97. niwrap_afni/afni/get_afni_model_prf_6_bad.py +212 -0
  98. niwrap_afni/afni/gifti_tool.py +426 -0
  99. niwrap_afni/afni/gltsymtest.py +193 -0
  100. niwrap_afni/afni/help_format.py +176 -0
  101. niwrap_afni/afni/im2niml.py +178 -0
  102. niwrap_afni/afni/images_equal.py +195 -0
  103. niwrap_afni/afni/imand.py +203 -0
  104. niwrap_afni/afni/imaver.py +201 -0
  105. niwrap_afni/afni/imcalc.py +235 -0
  106. niwrap_afni/afni/imcat.py +498 -0
  107. niwrap_afni/afni/imcutup.py +241 -0
  108. niwrap_afni/afni/imdump.py +177 -0
  109. niwrap_afni/afni/immask.py +223 -0
  110. niwrap_afni/afni/imreg.py +389 -0
  111. niwrap_afni/afni/imrotate.py +217 -0
  112. niwrap_afni/afni/imstack.py +209 -0
  113. niwrap_afni/afni/imstat.py +217 -0
  114. niwrap_afni/afni/imupsam.py +205 -0
  115. niwrap_afni/afni/init_user_dotfiles_py.py +353 -0
  116. niwrap_afni/afni/inspec.py +255 -0
  117. niwrap_afni/afni/iso_surface.py +344 -0
  118. niwrap_afni/afni/make_color_map.py +417 -0
  119. niwrap_afni/afni/make_pq_script_py.py +200 -0
  120. niwrap_afni/afni/make_random_timing_py.py +471 -0
  121. niwrap_afni/afni/make_stim_times_py.py +304 -0
  122. niwrap_afni/afni/map_icosahedron.py +296 -0
  123. niwrap_afni/afni/map_track_id.py +254 -0
  124. niwrap_afni/afni/mba.py +360 -0
  125. niwrap_afni/afni/meica_py.py +259 -0
  126. niwrap_afni/afni/myget.py +186 -0
  127. niwrap_afni/afni/neuro_deconvolve_py.py +291 -0
  128. niwrap_afni/afni/nicat.py +207 -0
  129. niwrap_afni/afni/niccc.py +307 -0
  130. niwrap_afni/afni/nifti_tool.py +310 -0
  131. niwrap_afni/afni/niml_feedme.py +260 -0
  132. niwrap_afni/afni/nsize.py +184 -0
  133. niwrap_afni/afni/p2dsetstat.py +216 -0
  134. niwrap_afni/afni/parse_fs_lt_log_py.py +217 -0
  135. niwrap_afni/afni/plugout_drive.py +259 -0
  136. niwrap_afni/afni/plugout_ijk.py +297 -0
  137. niwrap_afni/afni/plugout_tt.py +326 -0
  138. niwrap_afni/afni/plugout_tta.py +290 -0
  139. niwrap_afni/afni/prompt_popup.py +205 -0
  140. niwrap_afni/afni/prompt_user.py +190 -0
  141. niwrap_afni/afni/pta.py +279 -0
  142. niwrap_afni/afni/qdelaunay.py +534 -0
  143. niwrap_afni/afni/qhull.py +376 -0
  144. niwrap_afni/afni/quick_alpha_vals_py.py +189 -0
  145. niwrap_afni/afni/quickspec.py +259 -0
  146. niwrap_afni/afni/quickspec_sl.py +282 -0
  147. niwrap_afni/afni/quotize.py +194 -0
  148. niwrap_afni/afni/r_pkgs_install.py +227 -0
  149. niwrap_afni/afni/rba.py +508 -0
  150. niwrap_afni/afni/rbox.py +245 -0
  151. niwrap_afni/afni/read_matlab_files_py.py +225 -0
  152. niwrap_afni/afni/realtime_receiver.py +310 -0
  153. niwrap_afni/afni/retro_ts_py.py +477 -0
  154. niwrap_afni/afni/rmz.py +203 -0
  155. niwrap_afni/afni/roi2dataset.py +310 -0
  156. niwrap_afni/afni/roigrow.py +276 -0
  157. niwrap_afni/afni/rotcom.py +190 -0
  158. niwrap_afni/afni/rsfgen.py +330 -0
  159. niwrap_afni/afni/rtfeedme.py +308 -0
  160. niwrap_afni/afni/samp_bias.py +245 -0
  161. niwrap_afni/afni/scale_to_map.py +481 -0
  162. niwrap_afni/afni/serial_helper.py +298 -0
  163. niwrap_afni/afni/sfim.py +229 -0
  164. niwrap_afni/afni/slow_surf_clustsim_py.py +285 -0
  165. niwrap_afni/afni/spharm_deco.py +284 -0
  166. niwrap_afni/afni/spharm_reco.py +274 -0
  167. niwrap_afni/afni/stimband.py +229 -0
  168. niwrap_afni/afni/strblast.py +239 -0
  169. niwrap_afni/afni/suma_change_spec.py +225 -0
  170. niwrap_afni/afni/suma_glxdino.py +175 -0
  171. niwrap_afni/afni/surf2_vol_coord.py +305 -0
  172. niwrap_afni/afni/surf_clust.py +611 -0
  173. niwrap_afni/afni/surf_dist.py +208 -0
  174. niwrap_afni/afni/surf_dset_info.py +355 -0
  175. niwrap_afni/afni/surf_extrema.py +279 -0
  176. niwrap_afni/afni/surf_fwhm.py +350 -0
  177. niwrap_afni/afni/surf_info.py +288 -0
  178. niwrap_afni/afni/surf_layers.py +300 -0
  179. niwrap_afni/afni/surf_localstat.py +242 -0
  180. niwrap_afni/afni/surf_measures.py +373 -0
  181. niwrap_afni/afni/surf_mesh.py +256 -0
  182. niwrap_afni/afni/surf_patch.py +412 -0
  183. niwrap_afni/afni/surf_qual.py +250 -0
  184. niwrap_afni/afni/surf_retino_map.py +225 -0
  185. niwrap_afni/afni/surf_smooth.py +388 -0
  186. niwrap_afni/afni/surf_to_surf.py +327 -0
  187. niwrap_afni/afni/surface_metrics.py +377 -0
  188. niwrap_afni/afni/tedana_wrapper_py.py +306 -0
  189. niwrap_afni/afni/tfim.py +267 -0
  190. niwrap_afni/afni/timing_tool_py.py +406 -0
  191. niwrap_afni/afni/to3d.py +643 -0
  192. niwrap_afni/afni/tokens.py +192 -0
  193. niwrap_afni/afni/trr.py +405 -0
  194. niwrap_afni/afni/uber_align_test_py.py +266 -0
  195. niwrap_afni/afni/uber_proc_py.py +176 -0
  196. niwrap_afni/afni/uber_skel.py +277 -0
  197. niwrap_afni/afni/uber_subject_py.py +707 -0
  198. niwrap_afni/afni/un_warp_epi_py.py +232 -0
  199. niwrap_afni/afni/uniq_images.py +180 -0
  200. niwrap_afni/afni/v_1d_apar2mat.py +262 -0
  201. niwrap_afni/afni/v_1d_astrip.py +176 -0
  202. niwrap_afni/afni/v_1d_bandpass.py +238 -0
  203. niwrap_afni/afni/v_1d_bport.py +277 -0
  204. niwrap_afni/afni/v_1d_correlate.py +218 -0
  205. niwrap_afni/afni/v_1d_dw_grad_o_mat__.py +429 -0
  206. niwrap_afni/afni/v_1d_flag_motion.py +212 -0
  207. niwrap_afni/afni/v_1d_marry.py +214 -0
  208. niwrap_afni/afni/v_1d_nlfit.py +254 -0
  209. niwrap_afni/afni/v_1d_rplot.py +180 -0
  210. niwrap_afni/afni/v_1d_sem.py +215 -0
  211. niwrap_afni/afni/v_1d_tool_py.py +319 -0
  212. niwrap_afni/afni/v_1d_tsort.py +216 -0
  213. niwrap_afni/afni/v_1d_upsample.py +195 -0
  214. niwrap_afni/afni/v_1dcat.py +266 -0
  215. niwrap_afni/afni/v_1ddot.py +249 -0
  216. niwrap_afni/afni/v_1deval.py +265 -0
  217. niwrap_afni/afni/v_1dfft.py +269 -0
  218. niwrap_afni/afni/v_1dgen_arma11.py +319 -0
  219. niwrap_afni/afni/v_1dgrayplot.py +238 -0
  220. niwrap_afni/afni/v_1dmatcalc.py +180 -0
  221. niwrap_afni/afni/v_1dnorm.py +224 -0
  222. niwrap_afni/afni/v_1dplot.py +831 -0
  223. niwrap_afni/afni/v_1dplot_py.py +578 -0
  224. niwrap_afni/afni/v_1dsound.py +292 -0
  225. niwrap_afni/afni/v_1dsum.py +235 -0
  226. niwrap_afni/afni/v_1dsvd.py +272 -0
  227. niwrap_afni/afni/v_1dtranspose.py +188 -0
  228. niwrap_afni/afni/v_24swap.py +194 -0
  229. niwrap_afni/afni/v_2d_im_reg.py +312 -0
  230. niwrap_afni/afni/v_2dcat.py +496 -0
  231. niwrap_afni/afni/v_2perm.py +233 -0
  232. niwrap_afni/afni/v_2swap.py +181 -0
  233. niwrap_afni/afni/v_3_droimaker.py +419 -0
  234. niwrap_afni/afni/v_3d_aboverlap.py +211 -0
  235. niwrap_afni/afni/v_3d_acost.py +210 -0
  236. niwrap_afni/afni/v_3d_afnito3_d.py +177 -0
  237. niwrap_afni/afni/v_3d_afnito_analyze.py +219 -0
  238. niwrap_afni/afni/v_3d_afnito_nifti.py +245 -0
  239. niwrap_afni/afni/v_3d_afnito_niml.py +175 -0
  240. niwrap_afni/afni/v_3d_afnito_raw.py +202 -0
  241. niwrap_afni/afni/v_3d_allineate.py +350 -0
  242. niwrap_afni/afni/v_3d_amp_to_rsfc.py +262 -0
  243. niwrap_afni/afni/v_3d_anhist.py +260 -0
  244. niwrap_afni/afni/v_3d_anova.py +359 -0
  245. niwrap_afni/afni/v_3d_anova2.py +515 -0
  246. niwrap_afni/afni/v_3d_anova3.py +302 -0
  247. niwrap_afni/afni/v_3d_attribute.py +248 -0
  248. niwrap_afni/afni/v_3d_auto_tcorrelate.py +314 -0
  249. niwrap_afni/afni/v_3d_autobox.py +335 -0
  250. niwrap_afni/afni/v_3d_automask.py +258 -0
  251. niwrap_afni/afni/v_3d_ball_match.py +229 -0
  252. niwrap_afni/afni/v_3d_bandpass.py +381 -0
  253. niwrap_afni/afni/v_3d_blur_in_mask.py +291 -0
  254. niwrap_afni/afni/v_3d_blur_to_fwhm.py +267 -0
  255. niwrap_afni/afni/v_3d_brain_sync.py +267 -0
  256. niwrap_afni/afni/v_3d_brain_voyagerto_afni.py +313 -0
  257. niwrap_afni/afni/v_3d_brick_stat.py +463 -0
  258. niwrap_afni/afni/v_3d_clip_level.py +175 -0
  259. niwrap_afni/afni/v_3d_clust_count.py +229 -0
  260. niwrap_afni/afni/v_3d_clust_sim.py +196 -0
  261. niwrap_afni/afni/v_3d_clusterize.py +448 -0
  262. niwrap_afni/afni/v_3d_cm.py +177 -0
  263. niwrap_afni/afni/v_3d_compare_affine.py +215 -0
  264. niwrap_afni/afni/v_3d_conformist.py +176 -0
  265. niwrap_afni/afni/v_3d_convolve.py +197 -0
  266. niwrap_afni/afni/v_3d_cruiseto_afni.py +264 -0
  267. niwrap_afni/afni/v_3d_deconvolve.py +371 -0
  268. niwrap_afni/afni/v_3d_degree_centrality.py +270 -0
  269. niwrap_afni/afni/v_3d_depth_map.py +317 -0
  270. niwrap_afni/afni/v_3d_despike.py +191 -0
  271. niwrap_afni/afni/v_3d_detrend.py +191 -0
  272. niwrap_afni/afni/v_3d_dft.py +245 -0
  273. niwrap_afni/afni/v_3d_diff.py +254 -0
  274. niwrap_afni/afni/v_3d_dteig.py +236 -0
  275. niwrap_afni/afni/v_3d_dtto_dwi.py +199 -0
  276. niwrap_afni/afni/v_3d_dtto_noisy_dwi.py +275 -0
  277. niwrap_afni/afni/v_3d_dwito_dt.py +191 -0
  278. niwrap_afni/afni/v_3d_dwuncert.py +283 -0
  279. niwrap_afni/afni/v_3d_ecm.py +363 -0
  280. niwrap_afni/afni/v_3d_edu_01_scale.py +216 -0
  281. niwrap_afni/afni/v_3d_eigs_to_dt.py +271 -0
  282. niwrap_afni/afni/v_3d_empty.py +224 -0
  283. niwrap_afni/afni/v_3d_entropy.py +181 -0
  284. niwrap_afni/afni/v_3d_errts_cormat.py +243 -0
  285. niwrap_afni/afni/v_3d_exchange.py +226 -0
  286. niwrap_afni/afni/v_3d_extract_group_in_corr.py +195 -0
  287. niwrap_afni/afni/v_3d_extrema.py +384 -0
  288. niwrap_afni/afni/v_3d_fdr.py +325 -0
  289. niwrap_afni/afni/v_3d_fft.py +307 -0
  290. niwrap_afni/afni/v_3d_friedman.py +226 -0
  291. niwrap_afni/afni/v_3d_fwhmx.py +321 -0
  292. niwrap_afni/afni/v_3d_gen_feature_dist.py +262 -0
  293. niwrap_afni/afni/v_3d_gen_priors.py +487 -0
  294. niwrap_afni/afni/v_3d_getrow.py +243 -0
  295. niwrap_afni/afni/v_3d_grayplot.py +343 -0
  296. niwrap_afni/afni/v_3d_group_in_corr.py +484 -0
  297. niwrap_afni/afni/v_3d_hist.py +406 -0
  298. niwrap_afni/afni/v_3d_icc.py +228 -0
  299. niwrap_afni/afni/v_3d_intracranial.py +275 -0
  300. niwrap_afni/afni/v_3d_inv_fmri.py +317 -0
  301. niwrap_afni/afni/v_3d_isc.py +298 -0
  302. niwrap_afni/afni/v_3d_kruskal_wallis.py +231 -0
  303. niwrap_afni/afni/v_3d_lfcd.py +249 -0
  304. niwrap_afni/afni/v_3d_lme.py +524 -0
  305. niwrap_afni/afni/v_3d_lmer.py +425 -0
  306. niwrap_afni/afni/v_3d_local_acf.py +224 -0
  307. niwrap_afni/afni/v_3d_local_bistat.py +325 -0
  308. niwrap_afni/afni/v_3d_local_histog.py +268 -0
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  314. niwrap_afni/afni/v_3d_lrflip.py +202 -0
  315. niwrap_afni/afni/v_3d_lss.py +175 -0
  316. niwrap_afni/afni/v_3d_mann_whitney.py +234 -0
  317. niwrap_afni/afni/v_3d_mask_to_ascii.py +189 -0
  318. niwrap_afni/afni/v_3d_match.py +300 -0
  319. niwrap_afni/afni/v_3d_mean.py +364 -0
  320. niwrap_afni/afni/v_3d_median_filter.py +238 -0
  321. niwrap_afni/afni/v_3d_mema.py +171 -0
  322. niwrap_afni/afni/v_3d_mepfm.py +256 -0
  323. niwrap_afni/afni/v_3d_mse.py +283 -0
  324. niwrap_afni/afni/v_3d_mss.py +397 -0
  325. niwrap_afni/afni/v_3d_multi_thresh.py +306 -0
  326. niwrap_afni/afni/v_3d_mvm.py +359 -0
  327. niwrap_afni/afni/v_3d_mvm_validator.py +191 -0
  328. niwrap_afni/afni/v_3d_net_corr.py +398 -0
  329. niwrap_afni/afni/v_3d_nlfim.py +241 -0
  330. niwrap_afni/afni/v_3d_normality_test.py +209 -0
  331. niwrap_afni/afni/v_3d_notes.py +246 -0
  332. niwrap_afni/afni/v_3d_nwarp_adjust.py +218 -0
  333. niwrap_afni/afni/v_3d_nwarp_apply.py +349 -0
  334. niwrap_afni/afni/v_3d_nwarp_cat.py +277 -0
  335. niwrap_afni/afni/v_3d_nwarp_funcs.py +232 -0
  336. niwrap_afni/afni/v_3d_nwarp_xyz.py +193 -0
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  339. niwrap_afni/afni/v_3d_periodogram.py +220 -0
  340. niwrap_afni/afni/v_3d_pfm.py +248 -0
  341. niwrap_afni/afni/v_3d_polyfit.py +357 -0
  342. niwrap_afni/afni/v_3d_pval.py +232 -0
  343. niwrap_afni/afni/v_3d_pvmap.py +221 -0
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  345. niwrap_afni/afni/v_3d_rank.py +222 -0
  346. niwrap_afni/afni/v_3d_rankizer.py +241 -0
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  354. niwrap_afni/afni/v_3d_rsfc.py +198 -0
  355. niwrap_afni/afni/v_3d_seg.py +437 -0
  356. niwrap_afni/afni/v_3d_setup_group_in_corr.py +273 -0
  357. niwrap_afni/afni/v_3d_sharpen.py +206 -0
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  376. niwrap_afni/afni/v_3d_tortoiseto_here.py +239 -0
  377. niwrap_afni/afni/v_3d_toutcount.py +285 -0
  378. niwrap_afni/afni/v_3d_toy_prog.py +216 -0
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  380. niwrap_afni/afni/v_3d_tqual.py +261 -0
  381. niwrap_afni/afni/v_3d_track_id.py +628 -0
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  393. niwrap_afni/afni/v_3d_upsample.py +245 -0
  394. niwrap_afni/afni/v_3d_vec_rgb_to_hsl.py +226 -0
  395. niwrap_afni/afni/v_3d_vol2_surf.py +653 -0
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  397. niwrap_afni/afni/v_3d_warp_drive.py +596 -0
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  399. niwrap_afni/afni/v_3d_winsor.py +287 -0
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  402. niwrap_afni/afni/v_3d_zcat.py +259 -0
  403. niwrap_afni/afni/v_3d_zcutup.py +209 -0
  404. niwrap_afni/afni/v_3d_zeropad.py +371 -0
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  406. niwrap_afni/afni/v_3d_zregrid.py +242 -0
  407. niwrap_afni/afni/v_3danisosmooth.py +436 -0
  408. niwrap_afni/afni/v_3daxialize.py +253 -0
  409. niwrap_afni/afni/v_3dbucket.py +266 -0
  410. niwrap_afni/afni/v_3dcalc.py +278 -0
  411. niwrap_afni/afni/v_3dclust.py +380 -0
  412. niwrap_afni/afni/v_3dcopy.py +184 -0
  413. niwrap_afni/afni/v_3ddelay.py +443 -0
  414. niwrap_afni/afni/v_3ddot.py +322 -0
  415. niwrap_afni/afni/v_3ddot_beta.py +214 -0
  416. niwrap_afni/afni/v_3dedge3.py +269 -0
  417. niwrap_afni/afni/v_3dedgedog.py +344 -0
  418. niwrap_afni/afni/v_3dfim_.py +350 -0
  419. niwrap_afni/afni/v_3dfractionize.py +261 -0
  420. niwrap_afni/afni/v_3dhistog.py +365 -0
  421. niwrap_afni/afni/v_3dinfill.py +302 -0
  422. niwrap_afni/afni/v_3dinfo.py +1271 -0
  423. niwrap_afni/afni/v_3dkmeans.py +449 -0
  424. niwrap_afni/afni/v_3dmask_svd.py +179 -0
  425. niwrap_afni/afni/v_3dmask_tool.py +334 -0
  426. niwrap_afni/afni/v_3dmaskave.py +223 -0
  427. niwrap_afni/afni/v_3dmaskdump.py +425 -0
  428. niwrap_afni/afni/v_3dmatcalc.py +221 -0
  429. niwrap_afni/afni/v_3dmatmult.py +227 -0
  430. niwrap_afni/afni/v_3dmaxdisp.py +205 -0
  431. niwrap_afni/afni/v_3dmaxima.py +373 -0
  432. niwrap_afni/afni/v_3dmerge.py +305 -0
  433. niwrap_afni/afni/v_3dnewid.py +239 -0
  434. niwrap_afni/afni/v_3dnvals.py +190 -0
  435. niwrap_afni/afni/v_3dpc.py +340 -0
  436. niwrap_afni/afni/v_3drefit.py +406 -0
  437. niwrap_afni/afni/v_3drename.py +180 -0
  438. niwrap_afni/afni/v_3dresample.py +256 -0
  439. niwrap_afni/afni/v_3dretroicor.py +296 -0
  440. niwrap_afni/afni/v_3drotate.py +477 -0
  441. niwrap_afni/afni/v_3dsvm.py +518 -0
  442. niwrap_afni/afni/v_3dsvm_linpredict.py +203 -0
  443. niwrap_afni/afni/v_3dto_xdataset.py +195 -0
  444. niwrap_afni/afni/v_3dttest__.py +444 -0
  445. niwrap_afni/afni/v_3dvolreg.py +360 -0
  446. niwrap_afni/afni/v_4swap.py +181 -0
  447. niwrap_afni/afni/v__1d_diff_mag.py +178 -0
  448. niwrap_afni/afni/v__2dwarper.py +176 -0
  449. niwrap_afni/afni/v__2dwarper_allin.py +207 -0
  450. niwrap_afni/afni/v__4_daverage.py +173 -0
  451. niwrap_afni/afni/v__add_edge.py +344 -0
  452. niwrap_afni/afni/v__afni_env.py +254 -0
  453. niwrap_afni/afni/v__afni_orient2_raimap.py +172 -0
  454. niwrap_afni/afni/v__afni_orient_sign.py +179 -0
  455. niwrap_afni/afni/v__afni_r_package_install.py +241 -0
  456. niwrap_afni/afni/v__afni_refacer_make_master.py +180 -0
  457. niwrap_afni/afni/v__afni_refacer_make_onebig_a12.py +178 -0
  458. niwrap_afni/afni/v__afni_refacer_run.py +304 -0
  459. niwrap_afni/afni/v__afni_run_me.py +191 -0
  460. niwrap_afni/afni/v__align_centers.py +324 -0
  461. niwrap_afni/afni/v__align_partial_oblique.py +285 -0
  462. niwrap_afni/afni/v__anaticor.py +326 -0
  463. niwrap_afni/afni/v__animal_warper.py +602 -0
  464. niwrap_afni/afni/v__atlasize.py +402 -0
  465. niwrap_afni/afni/v__auto_tlrc.py +642 -0
  466. niwrap_afni/afni/v__build_afni_xlib.py +201 -0
  467. niwrap_afni/afni/v__center_distance.py +187 -0
  468. niwrap_afni/afni/v__chauffeur_afni.py +204 -0
  469. niwrap_afni/afni/v__check_for_afni_dset.py +178 -0
  470. niwrap_afni/afni/v__clip_volume.py +388 -0
  471. niwrap_afni/afni/v__clust_exp_cat_lab.py +201 -0
  472. niwrap_afni/afni/v__clust_exp_run_shiny.py +181 -0
  473. niwrap_afni/afni/v__command_globb.py +220 -0
  474. niwrap_afni/afni/v__compute_gcor.py +246 -0
  475. niwrap_afni/afni/v__compute_oc_weights.py +287 -0
  476. niwrap_afni/afni/v__deblank_file_names.py +210 -0
  477. niwrap_afni/afni/v__demo_prompt.py +176 -0
  478. niwrap_afni/afni/v__dice_metric.py +315 -0
  479. niwrap_afni/afni/v__diff_files.py +273 -0
  480. niwrap_afni/afni/v__diff_tree.py +358 -0
  481. niwrap_afni/afni/v__djunct_4d_imager.py +225 -0
  482. niwrap_afni/afni/v__djunct_4d_slices_to_3d_vol.py +177 -0
  483. niwrap_afni/afni/v__djunct_anonymize.py +207 -0
  484. niwrap_afni/afni/v__djunct_dwi_selector.py +192 -0
  485. niwrap_afni/afni/v__djunct_edgy_align_check.py +339 -0
  486. niwrap_afni/afni/v__djunct_modal_smoothing_with_rep.py +249 -0
  487. niwrap_afni/afni/v__djunct_montage_coordinator.py +234 -0
  488. niwrap_afni/afni/v__djunct_overlap_check.py +430 -0
  489. niwrap_afni/afni/v__djunct_ssw_intermed_edge_imgs.py +311 -0
  490. niwrap_afni/afni/v__do_examples.py +181 -0
  491. niwrap_afni/afni/v__electro_grid.py +244 -0
  492. niwrap_afni/afni/v__examine_gen_feat_dists.py +277 -0
  493. niwrap_afni/afni/v__extract_meica_ortvec.py +248 -0
  494. niwrap_afni/afni/v__fast_roi.py +290 -0
  495. niwrap_afni/afni/v__fat_tract_colorize.py +267 -0
  496. niwrap_afni/afni/v__find_afni_dset_path.py +199 -0
  497. niwrap_afni/afni/v__fix_fssphere.py +236 -0
  498. niwrap_afni/afni/v__float_fix.py +176 -0
  499. niwrap_afni/afni/v__from_rai.py +186 -0
  500. niwrap_afni/afni/v__fs_roi_label.py +290 -0
  501. niwrap_afni/afni/v__fslabel2dset.py +217 -0
  502. niwrap_afni/afni/v__get_afni_dims.py +176 -0
  503. niwrap_afni/afni/v__get_afni_id.py +176 -0
  504. niwrap_afni/afni/v__get_afni_orient.py +185 -0
  505. niwrap_afni/afni/v__get_afni_prefix.py +182 -0
  506. niwrap_afni/afni/v__get_afni_res.py +183 -0
  507. niwrap_afni/afni/v__get_afni_version.py +177 -0
  508. niwrap_afni/afni/v__get_afni_view.py +178 -0
  509. niwrap_afni/afni/v__grad_flip_test.py +359 -0
  510. niwrap_afni/afni/v__grayplot.py +189 -0
  511. niwrap_afni/afni/v__help_afni.py +165 -0
  512. niwrap_afni/afni/v__is_oblique.py +176 -0
  513. niwrap_afni/afni/v__iso_masks.py +185 -0
  514. niwrap_afni/afni/v__make_label_table.py +587 -0
  515. niwrap_afni/afni/v__make_plug_diff.py +237 -0
  516. niwrap_afni/afni/v__measure_bb_thick.py +352 -0
  517. niwrap_afni/afni/v__measure_erosion_thick.py +328 -0
  518. niwrap_afni/afni/v__measure_in2out.py +355 -0
  519. niwrap_afni/afni/v__move_to_series_dirs.py +255 -0
  520. niwrap_afni/afni/v__no_ext.py +179 -0
  521. niwrap_afni/afni/v__no_pound.py +174 -0
  522. niwrap_afni/afni/v__noisy_skull_strip.py +212 -0
  523. niwrap_afni/afni/v__np.py +180 -0
  524. niwrap_afni/afni/v__parse_afni_name.py +187 -0
  525. niwrap_afni/afni/v__purify_1_d.py +202 -0
  526. niwrap_afni/afni/v__quiet_talkers.py +256 -0
  527. niwrap_afni/afni/v__radial_correlate.py +407 -0
  528. niwrap_afni/afni/v__rename_panga.py +279 -0
  529. niwrap_afni/afni/v__reorder.py +225 -0
  530. niwrap_afni/afni/v__retino_proc.py +670 -0
  531. niwrap_afni/afni/v__roi_corr_mat.py +277 -0
  532. niwrap_afni/afni/v__roi_decluster.py +252 -0
  533. niwrap_afni/afni/v__roi_modal_grow.py +256 -0
  534. niwrap_afni/afni/v__scale_volume.py +252 -0
  535. niwrap_afni/afni/v__script_check.py +201 -0
  536. niwrap_afni/afni/v__shift_volume.py +240 -0
  537. niwrap_afni/afni/v__show_dynamic_range.py +183 -0
  538. niwrap_afni/afni/v__simulate_motion.py +350 -0
  539. niwrap_afni/afni/v__skull_strip_touch_up.py +224 -0
  540. niwrap_afni/afni/v__snapshot_volreg.py +207 -0
  541. niwrap_afni/afni/v__spharm_examples.py +226 -0
  542. niwrap_afni/afni/v__sswarper.py +465 -0
  543. niwrap_afni/afni/v__statauxcode.py +178 -0
  544. niwrap_afni/afni/v__suma_acknowledge.py +259 -0
  545. niwrap_afni/afni/v__suma_align_to_experiment.py +421 -0
  546. niwrap_afni/afni/v__suma_fsvol_to_brik.py +189 -0
  547. niwrap_afni/afni/v__suma_make_spec_caret.py +183 -0
  548. niwrap_afni/afni/v__suma_make_spec_fs.py +180 -0
  549. niwrap_afni/afni/v__suma_make_spec_sf.py +207 -0
  550. niwrap_afni/afni/v__suma_renumber_fs.py +209 -0
  551. niwrap_afni/afni/v__suma_reprefixize_spec.py +221 -0
  552. niwrap_afni/afni/v__surf_smooth_heat_07_examples.py +172 -0
  553. niwrap_afni/afni/v__surf_to_vol_spackle.py +322 -0
  554. niwrap_afni/afni/v__t1scale.py +328 -0
  555. niwrap_afni/afni/v__thickness_master.py +213 -0
  556. niwrap_afni/afni/v__time_diff.py +180 -0
  557. niwrap_afni/afni/v__to_mni_awarp.py +188 -0
  558. niwrap_afni/afni/v__to_mni_qwarpar.py +170 -0
  559. niwrap_afni/afni/v__to_rai.py +170 -0
  560. niwrap_afni/afni/v__update_afni_binaries.py +410 -0
  561. niwrap_afni/afni/v__vol_center.py +188 -0
  562. niwrap_afni/afni/v__xyz_to_ijk.py +221 -0
  563. niwrap_afni/afni/vecwarp.py +265 -0
  564. niwrap_afni/afni/waver.py +458 -0
  565. niwrap_afni/afni/whirlgif.py +254 -0
  566. niwrap_afni/afni/xmat_tool_py.py +381 -0
  567. niwrap_afni-0.5.0.dist-info/METADATA +8 -0
  568. niwrap_afni-0.5.0.dist-info/RECORD +569 -0
  569. niwrap_afni-0.5.0.dist-info/WHEEL +4 -0
@@ -0,0 +1,707 @@
1
+ # This file was auto generated by Styx.
2
+ # Do not edit this file directly.
3
+
4
+ import typing
5
+ import pathlib
6
+ from styxdefs import *
7
+
8
+ UBER_SUBJECT_PY_METADATA = Metadata(
9
+ id="d4f27b8c1311827036baefee6a5e5f22311c1cf3.boutiques",
10
+ name="uber_subject.py",
11
+ package="afni",
12
+ container_image_tag="afni/afni_make_build:AFNI_24.2.06",
13
+ )
14
+
15
+
16
+ UberSubjectPyParameters = typing.TypedDict('UberSubjectPyParameters', {
17
+ "__STYX_TYPE__": typing.Literal["uber_subject.py"],
18
+ "qt_opts": typing.NotRequired[str | None],
19
+ "svar": typing.NotRequired[str | None],
20
+ "cvar": typing.NotRequired[str | None],
21
+ "no_gui": bool,
22
+ "print_ap_command": bool,
23
+ "save_ap_command": typing.NotRequired[str | None],
24
+ "exec_ap_command": bool,
25
+ "exec_proc_script": bool,
26
+ "align_cost": typing.NotRequired[str | None],
27
+ "align_giant_move": typing.NotRequired[str | None],
28
+ "align_opts_aea": typing.NotRequired[str | None],
29
+ "anal_domain": typing.NotRequired[str | None],
30
+ "anal_type": typing.NotRequired[str | None],
31
+ "anat": typing.NotRequired[InputPathType | None],
32
+ "anat_has_skull": typing.NotRequired[str | None],
33
+ "blocks": typing.NotRequired[str | None],
34
+ "blur_size": typing.NotRequired[float | None],
35
+ "epi": typing.NotRequired[str | None],
36
+ "epi_wildcard": typing.NotRequired[str | None],
37
+ "gid": typing.NotRequired[str | None],
38
+ "gltsym": typing.NotRequired[str | None],
39
+ "gltsym_label": typing.NotRequired[str | None],
40
+ "motion_limit": typing.NotRequired[float | None],
41
+ "outlier_limit": typing.NotRequired[float | None],
42
+ "regress_GOFORIT": typing.NotRequired[float | None],
43
+ "regress_bandpass": typing.NotRequired[str | None],
44
+ "regress_jobs": typing.NotRequired[float | None],
45
+ "regress_mot_deriv": typing.NotRequired[str | None],
46
+ "regress_opts_3dD": typing.NotRequired[str | None],
47
+ "reml_exec": typing.NotRequired[str | None],
48
+ "run_clustsim": typing.NotRequired[str | None],
49
+ "sid": typing.NotRequired[str | None],
50
+ "stim": typing.NotRequired[InputPathType | None],
51
+ "stim_basis": typing.NotRequired[str | None],
52
+ "stim_label": typing.NotRequired[str | None],
53
+ "stim_type": typing.NotRequired[str | None],
54
+ "stim_wildcard": typing.NotRequired[str | None],
55
+ "tcat_nfirst": typing.NotRequired[float | None],
56
+ "tlrc_base": typing.NotRequired[str | None],
57
+ "tlrc_ok_maxite": typing.NotRequired[str | None],
58
+ "tlrc_opts_at": typing.NotRequired[str | None],
59
+ "volreg_base": typing.NotRequired[str | None],
60
+ "verb": typing.NotRequired[str | None],
61
+ })
62
+
63
+
64
+ def dyn_cargs(
65
+ t: str,
66
+ ) -> typing.Any:
67
+ """
68
+ Get build cargs function by command type.
69
+
70
+ Args:
71
+ t: Command type.
72
+ Returns:
73
+ Build cargs function.
74
+ """
75
+ return {
76
+ "uber_subject.py": uber_subject_py_cargs,
77
+ }.get(t)
78
+
79
+
80
+ def dyn_outputs(
81
+ t: str,
82
+ ) -> typing.Any:
83
+ """
84
+ Get build outputs function by command type.
85
+
86
+ Args:
87
+ t: Command type.
88
+ Returns:
89
+ Build outputs function.
90
+ """
91
+ return {
92
+ }.get(t)
93
+
94
+
95
+ class UberSubjectPyOutputs(typing.NamedTuple):
96
+ """
97
+ Output object returned when calling `uber_subject_py(...)`.
98
+ """
99
+ root: OutputPathType
100
+ """Output root folder. This is the root folder for all outputs."""
101
+
102
+
103
+ def uber_subject_py_params(
104
+ qt_opts: str | None = None,
105
+ svar: str | None = None,
106
+ cvar: str | None = None,
107
+ no_gui: bool = False,
108
+ print_ap_command: bool = False,
109
+ save_ap_command: str | None = None,
110
+ exec_ap_command: bool = False,
111
+ exec_proc_script: bool = False,
112
+ align_cost: str | None = None,
113
+ align_giant_move: str | None = None,
114
+ align_opts_aea: str | None = None,
115
+ anal_domain: str | None = None,
116
+ anal_type: str | None = None,
117
+ anat: InputPathType | None = None,
118
+ anat_has_skull: str | None = None,
119
+ blocks: str | None = None,
120
+ blur_size: float | None = None,
121
+ epi: str | None = None,
122
+ epi_wildcard: str | None = None,
123
+ gid: str | None = None,
124
+ gltsym: str | None = None,
125
+ gltsym_label: str | None = None,
126
+ motion_limit: float | None = None,
127
+ outlier_limit: float | None = None,
128
+ regress_goforit: float | None = None,
129
+ regress_bandpass: str | None = None,
130
+ regress_jobs: float | None = None,
131
+ regress_mot_deriv: str | None = None,
132
+ regress_opts_3d_d: str | None = None,
133
+ reml_exec: str | None = None,
134
+ run_clustsim: str | None = None,
135
+ sid: str | None = None,
136
+ stim: InputPathType | None = None,
137
+ stim_basis: str | None = None,
138
+ stim_label: str | None = None,
139
+ stim_type: str | None = None,
140
+ stim_wildcard: str | None = None,
141
+ tcat_nfirst: float | None = None,
142
+ tlrc_base: str | None = None,
143
+ tlrc_ok_maxite: str | None = None,
144
+ tlrc_opts_at: str | None = None,
145
+ volreg_base: str | None = None,
146
+ verb: str | None = None,
147
+ ) -> UberSubjectPyParameters:
148
+ """
149
+ Build parameters.
150
+
151
+ Args:
152
+ qt_opts: Pass options to PyQt4.
153
+ svar: Set subject variable to value.
154
+ cvar: Set control variable to value.
155
+ no_gui: Do not open graphical interface.
156
+ print_ap_command: Show afni_proc.py script.
157
+ save_ap_command: Save afni_proc.py script.
158
+ exec_ap_command: Run afni_proc.py command.
159
+ exec_proc_script: Run proc script.
160
+ align_cost: Specify cost function for anat/EPI alignment.
161
+ align_giant_move: Use -giant_move in AEA.py.
162
+ align_opts_aea: Specify extra options for align_epi_anat.py.
163
+ anal_domain: Set data domain (volume/rest).
164
+ anal_type: Set analysis type (task/rest).
165
+ anat: Set anatomical dataset name.
166
+ anat_has_skull: Whether anat has skull (yes/no).
167
+ blocks: Set list of processing blocks to apply.
168
+ blur_size: Set blur size in mm.
169
+ epi: Set list of EPI datasets.
170
+ epi_wildcard: Use wildcard for EPI datasets (yes/no).
171
+ gid: Set group ID.
172
+ gltsym: Specify list of symbolic GLTs.
173
+ gltsym_label: Set corresponding GLT labels.
174
+ motion_limit: Set per-TR motion limit in mm.
175
+ outlier_limit: Specify outlier limit for censoring.
176
+ regress_goforit: Set GOFORIT level in 3dDeconvolve.
177
+ regress_bandpass: Specify bandpass limits to remain after regress.
178
+ regress_jobs: Number of jobs to use in 3dDeconvolve.
179
+ regress_mot_deriv: Regress motion derivatives (yes/no).
180
+ regress_opts_3d_d: Specify extra options for 3dDeconvolve.
181
+ reml_exec: Run 3dREMLfit (yes/no).
182
+ run_clustsim: Run 3dClustSim (yes/no).
183
+ sid: Set subject ID.
184
+ stim: Set list of stim timing files.
185
+ stim_basis: Set basis functions for stim classes.
186
+ stim_label: Set stim file labels.
187
+ stim_type: Set stim types for stim classes.
188
+ stim_wildcard: Use wildcard for stim files (yes/no).
189
+ tcat_nfirst: Set number of TRs to remove per run.
190
+ tlrc_base: Specify anat for standard space alignment.
191
+ tlrc_ok_maxite: Pass -OK_maxite to @auto_tlrc (yes/no).
192
+ tlrc_opts_at: Specify extra options for @auto_tlrc.
193
+ volreg_base: Set volreg base string (first/third/last).
194
+ verb: Set verbose level.
195
+ Returns:
196
+ Parameter dictionary
197
+ """
198
+ params = {
199
+ "__STYXTYPE__": "uber_subject.py",
200
+ "no_gui": no_gui,
201
+ "print_ap_command": print_ap_command,
202
+ "exec_ap_command": exec_ap_command,
203
+ "exec_proc_script": exec_proc_script,
204
+ }
205
+ if qt_opts is not None:
206
+ params["qt_opts"] = qt_opts
207
+ if svar is not None:
208
+ params["svar"] = svar
209
+ if cvar is not None:
210
+ params["cvar"] = cvar
211
+ if save_ap_command is not None:
212
+ params["save_ap_command"] = save_ap_command
213
+ if align_cost is not None:
214
+ params["align_cost"] = align_cost
215
+ if align_giant_move is not None:
216
+ params["align_giant_move"] = align_giant_move
217
+ if align_opts_aea is not None:
218
+ params["align_opts_aea"] = align_opts_aea
219
+ if anal_domain is not None:
220
+ params["anal_domain"] = anal_domain
221
+ if anal_type is not None:
222
+ params["anal_type"] = anal_type
223
+ if anat is not None:
224
+ params["anat"] = anat
225
+ if anat_has_skull is not None:
226
+ params["anat_has_skull"] = anat_has_skull
227
+ if blocks is not None:
228
+ params["blocks"] = blocks
229
+ if blur_size is not None:
230
+ params["blur_size"] = blur_size
231
+ if epi is not None:
232
+ params["epi"] = epi
233
+ if epi_wildcard is not None:
234
+ params["epi_wildcard"] = epi_wildcard
235
+ if gid is not None:
236
+ params["gid"] = gid
237
+ if gltsym is not None:
238
+ params["gltsym"] = gltsym
239
+ if gltsym_label is not None:
240
+ params["gltsym_label"] = gltsym_label
241
+ if motion_limit is not None:
242
+ params["motion_limit"] = motion_limit
243
+ if outlier_limit is not None:
244
+ params["outlier_limit"] = outlier_limit
245
+ if regress_goforit is not None:
246
+ params["regress_GOFORIT"] = regress_goforit
247
+ if regress_bandpass is not None:
248
+ params["regress_bandpass"] = regress_bandpass
249
+ if regress_jobs is not None:
250
+ params["regress_jobs"] = regress_jobs
251
+ if regress_mot_deriv is not None:
252
+ params["regress_mot_deriv"] = regress_mot_deriv
253
+ if regress_opts_3d_d is not None:
254
+ params["regress_opts_3dD"] = regress_opts_3d_d
255
+ if reml_exec is not None:
256
+ params["reml_exec"] = reml_exec
257
+ if run_clustsim is not None:
258
+ params["run_clustsim"] = run_clustsim
259
+ if sid is not None:
260
+ params["sid"] = sid
261
+ if stim is not None:
262
+ params["stim"] = stim
263
+ if stim_basis is not None:
264
+ params["stim_basis"] = stim_basis
265
+ if stim_label is not None:
266
+ params["stim_label"] = stim_label
267
+ if stim_type is not None:
268
+ params["stim_type"] = stim_type
269
+ if stim_wildcard is not None:
270
+ params["stim_wildcard"] = stim_wildcard
271
+ if tcat_nfirst is not None:
272
+ params["tcat_nfirst"] = tcat_nfirst
273
+ if tlrc_base is not None:
274
+ params["tlrc_base"] = tlrc_base
275
+ if tlrc_ok_maxite is not None:
276
+ params["tlrc_ok_maxite"] = tlrc_ok_maxite
277
+ if tlrc_opts_at is not None:
278
+ params["tlrc_opts_at"] = tlrc_opts_at
279
+ if volreg_base is not None:
280
+ params["volreg_base"] = volreg_base
281
+ if verb is not None:
282
+ params["verb"] = verb
283
+ return params
284
+
285
+
286
+ def uber_subject_py_cargs(
287
+ params: UberSubjectPyParameters,
288
+ execution: Execution,
289
+ ) -> list[str]:
290
+ """
291
+ Build command-line arguments from parameters.
292
+
293
+ Args:
294
+ params: The parameters.
295
+ execution: The execution object for resolving input paths.
296
+ Returns:
297
+ Command-line arguments.
298
+ """
299
+ cargs = []
300
+ cargs.append("uber_subject.py")
301
+ if params.get("qt_opts") is not None:
302
+ cargs.extend([
303
+ "-qt_opts",
304
+ params.get("qt_opts")
305
+ ])
306
+ if params.get("svar") is not None:
307
+ cargs.extend([
308
+ "-svar",
309
+ params.get("svar")
310
+ ])
311
+ if params.get("cvar") is not None:
312
+ cargs.extend([
313
+ "-cvar",
314
+ params.get("cvar")
315
+ ])
316
+ if params.get("no_gui"):
317
+ cargs.append("-no_gui")
318
+ if params.get("print_ap_command"):
319
+ cargs.append("-print_ap_command")
320
+ if params.get("save_ap_command") is not None:
321
+ cargs.extend([
322
+ "-save_ap_command",
323
+ params.get("save_ap_command")
324
+ ])
325
+ if params.get("exec_ap_command"):
326
+ cargs.append("-exec_ap_command")
327
+ if params.get("exec_proc_script"):
328
+ cargs.append("-exec_proc_script")
329
+ if params.get("align_cost") is not None:
330
+ cargs.extend([
331
+ "-align_cost",
332
+ params.get("align_cost")
333
+ ])
334
+ if params.get("align_giant_move") is not None:
335
+ cargs.extend([
336
+ "-align_giant_move",
337
+ params.get("align_giant_move")
338
+ ])
339
+ if params.get("align_opts_aea") is not None:
340
+ cargs.extend([
341
+ "-align_opts_aea",
342
+ params.get("align_opts_aea")
343
+ ])
344
+ if params.get("anal_domain") is not None:
345
+ cargs.extend([
346
+ "-anal_domain",
347
+ params.get("anal_domain")
348
+ ])
349
+ if params.get("anal_type") is not None:
350
+ cargs.extend([
351
+ "-anal_type",
352
+ params.get("anal_type")
353
+ ])
354
+ if params.get("anat") is not None:
355
+ cargs.extend([
356
+ "-anat",
357
+ execution.input_file(params.get("anat"))
358
+ ])
359
+ if params.get("anat_has_skull") is not None:
360
+ cargs.extend([
361
+ "-anat_has_skull",
362
+ params.get("anat_has_skull")
363
+ ])
364
+ if params.get("blocks") is not None:
365
+ cargs.extend([
366
+ "-blocks",
367
+ params.get("blocks")
368
+ ])
369
+ if params.get("blur_size") is not None:
370
+ cargs.extend([
371
+ "-blur_size",
372
+ str(params.get("blur_size"))
373
+ ])
374
+ if params.get("epi") is not None:
375
+ cargs.extend([
376
+ "-epi",
377
+ params.get("epi")
378
+ ])
379
+ if params.get("epi_wildcard") is not None:
380
+ cargs.extend([
381
+ "-epi_wildcard",
382
+ params.get("epi_wildcard")
383
+ ])
384
+ if params.get("gid") is not None:
385
+ cargs.extend([
386
+ "-gid",
387
+ params.get("gid")
388
+ ])
389
+ if params.get("gltsym") is not None:
390
+ cargs.extend([
391
+ "-gltsym",
392
+ params.get("gltsym")
393
+ ])
394
+ if params.get("gltsym_label") is not None:
395
+ cargs.extend([
396
+ "-gltsym_label",
397
+ params.get("gltsym_label")
398
+ ])
399
+ if params.get("motion_limit") is not None:
400
+ cargs.extend([
401
+ "-motion_limit",
402
+ str(params.get("motion_limit"))
403
+ ])
404
+ if params.get("outlier_limit") is not None:
405
+ cargs.extend([
406
+ "-outlier_limit",
407
+ str(params.get("outlier_limit"))
408
+ ])
409
+ if params.get("regress_GOFORIT") is not None:
410
+ cargs.extend([
411
+ "-regress_GOFORIT",
412
+ str(params.get("regress_GOFORIT"))
413
+ ])
414
+ if params.get("regress_bandpass") is not None:
415
+ cargs.extend([
416
+ "-regress_bandpass",
417
+ params.get("regress_bandpass")
418
+ ])
419
+ if params.get("regress_jobs") is not None:
420
+ cargs.extend([
421
+ "-regress_jobs",
422
+ str(params.get("regress_jobs"))
423
+ ])
424
+ if params.get("regress_mot_deriv") is not None:
425
+ cargs.extend([
426
+ "-regress_mot_deriv",
427
+ params.get("regress_mot_deriv")
428
+ ])
429
+ if params.get("regress_opts_3dD") is not None:
430
+ cargs.extend([
431
+ "-regress_opts_3dD",
432
+ params.get("regress_opts_3dD")
433
+ ])
434
+ if params.get("reml_exec") is not None:
435
+ cargs.extend([
436
+ "-reml_exec",
437
+ params.get("reml_exec")
438
+ ])
439
+ if params.get("run_clustsim") is not None:
440
+ cargs.extend([
441
+ "-run_clustsim",
442
+ params.get("run_clustsim")
443
+ ])
444
+ if params.get("sid") is not None:
445
+ cargs.extend([
446
+ "-sid",
447
+ params.get("sid")
448
+ ])
449
+ if params.get("stim") is not None:
450
+ cargs.extend([
451
+ "-stim",
452
+ execution.input_file(params.get("stim"))
453
+ ])
454
+ if params.get("stim_basis") is not None:
455
+ cargs.extend([
456
+ "-stim_basis",
457
+ params.get("stim_basis")
458
+ ])
459
+ if params.get("stim_label") is not None:
460
+ cargs.extend([
461
+ "-stim_label",
462
+ params.get("stim_label")
463
+ ])
464
+ if params.get("stim_type") is not None:
465
+ cargs.extend([
466
+ "-stim_type",
467
+ params.get("stim_type")
468
+ ])
469
+ if params.get("stim_wildcard") is not None:
470
+ cargs.extend([
471
+ "-stim_wildcard",
472
+ params.get("stim_wildcard")
473
+ ])
474
+ if params.get("tcat_nfirst") is not None:
475
+ cargs.extend([
476
+ "-tcat_nfirst",
477
+ str(params.get("tcat_nfirst"))
478
+ ])
479
+ if params.get("tlrc_base") is not None:
480
+ cargs.extend([
481
+ "-tlrc_base",
482
+ params.get("tlrc_base")
483
+ ])
484
+ if params.get("tlrc_ok_maxite") is not None:
485
+ cargs.extend([
486
+ "-tlrc_ok_maxite",
487
+ params.get("tlrc_ok_maxite")
488
+ ])
489
+ if params.get("tlrc_opts_at") is not None:
490
+ cargs.extend([
491
+ "-tlrc_opts_at",
492
+ params.get("tlrc_opts_at")
493
+ ])
494
+ if params.get("volreg_base") is not None:
495
+ cargs.extend([
496
+ "-volreg_base",
497
+ params.get("volreg_base")
498
+ ])
499
+ if params.get("verb") is not None:
500
+ cargs.extend([
501
+ "-verb",
502
+ params.get("verb")
503
+ ])
504
+ return cargs
505
+
506
+
507
+ def uber_subject_py_outputs(
508
+ params: UberSubjectPyParameters,
509
+ execution: Execution,
510
+ ) -> UberSubjectPyOutputs:
511
+ """
512
+ Build outputs object containing output file paths and possibly stdout/stderr.
513
+
514
+ Args:
515
+ params: The parameters.
516
+ execution: The execution object for resolving input paths.
517
+ Returns:
518
+ Outputs object.
519
+ """
520
+ ret = UberSubjectPyOutputs(
521
+ root=execution.output_file("."),
522
+ )
523
+ return ret
524
+
525
+
526
+ def uber_subject_py_execute(
527
+ params: UberSubjectPyParameters,
528
+ execution: Execution,
529
+ ) -> UberSubjectPyOutputs:
530
+ """
531
+ Graphical interface to afni_proc.py.
532
+
533
+ Author: AFNI Developers
534
+
535
+ URL: https://afni.nimh.nih.gov/
536
+
537
+ Args:
538
+ params: The parameters.
539
+ execution: The execution object.
540
+ Returns:
541
+ NamedTuple of outputs (described in `UberSubjectPyOutputs`).
542
+ """
543
+ params = execution.params(params)
544
+ cargs = uber_subject_py_cargs(params, execution)
545
+ ret = uber_subject_py_outputs(params, execution)
546
+ execution.run(cargs)
547
+ return ret
548
+
549
+
550
+ def uber_subject_py(
551
+ qt_opts: str | None = None,
552
+ svar: str | None = None,
553
+ cvar: str | None = None,
554
+ no_gui: bool = False,
555
+ print_ap_command: bool = False,
556
+ save_ap_command: str | None = None,
557
+ exec_ap_command: bool = False,
558
+ exec_proc_script: bool = False,
559
+ align_cost: str | None = None,
560
+ align_giant_move: str | None = None,
561
+ align_opts_aea: str | None = None,
562
+ anal_domain: str | None = None,
563
+ anal_type: str | None = None,
564
+ anat: InputPathType | None = None,
565
+ anat_has_skull: str | None = None,
566
+ blocks: str | None = None,
567
+ blur_size: float | None = None,
568
+ epi: str | None = None,
569
+ epi_wildcard: str | None = None,
570
+ gid: str | None = None,
571
+ gltsym: str | None = None,
572
+ gltsym_label: str | None = None,
573
+ motion_limit: float | None = None,
574
+ outlier_limit: float | None = None,
575
+ regress_goforit: float | None = None,
576
+ regress_bandpass: str | None = None,
577
+ regress_jobs: float | None = None,
578
+ regress_mot_deriv: str | None = None,
579
+ regress_opts_3d_d: str | None = None,
580
+ reml_exec: str | None = None,
581
+ run_clustsim: str | None = None,
582
+ sid: str | None = None,
583
+ stim: InputPathType | None = None,
584
+ stim_basis: str | None = None,
585
+ stim_label: str | None = None,
586
+ stim_type: str | None = None,
587
+ stim_wildcard: str | None = None,
588
+ tcat_nfirst: float | None = None,
589
+ tlrc_base: str | None = None,
590
+ tlrc_ok_maxite: str | None = None,
591
+ tlrc_opts_at: str | None = None,
592
+ volreg_base: str | None = None,
593
+ verb: str | None = None,
594
+ runner: Runner | None = None,
595
+ ) -> UberSubjectPyOutputs:
596
+ """
597
+ Graphical interface to afni_proc.py.
598
+
599
+ Author: AFNI Developers
600
+
601
+ URL: https://afni.nimh.nih.gov/
602
+
603
+ Args:
604
+ qt_opts: Pass options to PyQt4.
605
+ svar: Set subject variable to value.
606
+ cvar: Set control variable to value.
607
+ no_gui: Do not open graphical interface.
608
+ print_ap_command: Show afni_proc.py script.
609
+ save_ap_command: Save afni_proc.py script.
610
+ exec_ap_command: Run afni_proc.py command.
611
+ exec_proc_script: Run proc script.
612
+ align_cost: Specify cost function for anat/EPI alignment.
613
+ align_giant_move: Use -giant_move in AEA.py.
614
+ align_opts_aea: Specify extra options for align_epi_anat.py.
615
+ anal_domain: Set data domain (volume/rest).
616
+ anal_type: Set analysis type (task/rest).
617
+ anat: Set anatomical dataset name.
618
+ anat_has_skull: Whether anat has skull (yes/no).
619
+ blocks: Set list of processing blocks to apply.
620
+ blur_size: Set blur size in mm.
621
+ epi: Set list of EPI datasets.
622
+ epi_wildcard: Use wildcard for EPI datasets (yes/no).
623
+ gid: Set group ID.
624
+ gltsym: Specify list of symbolic GLTs.
625
+ gltsym_label: Set corresponding GLT labels.
626
+ motion_limit: Set per-TR motion limit in mm.
627
+ outlier_limit: Specify outlier limit for censoring.
628
+ regress_goforit: Set GOFORIT level in 3dDeconvolve.
629
+ regress_bandpass: Specify bandpass limits to remain after regress.
630
+ regress_jobs: Number of jobs to use in 3dDeconvolve.
631
+ regress_mot_deriv: Regress motion derivatives (yes/no).
632
+ regress_opts_3d_d: Specify extra options for 3dDeconvolve.
633
+ reml_exec: Run 3dREMLfit (yes/no).
634
+ run_clustsim: Run 3dClustSim (yes/no).
635
+ sid: Set subject ID.
636
+ stim: Set list of stim timing files.
637
+ stim_basis: Set basis functions for stim classes.
638
+ stim_label: Set stim file labels.
639
+ stim_type: Set stim types for stim classes.
640
+ stim_wildcard: Use wildcard for stim files (yes/no).
641
+ tcat_nfirst: Set number of TRs to remove per run.
642
+ tlrc_base: Specify anat for standard space alignment.
643
+ tlrc_ok_maxite: Pass -OK_maxite to @auto_tlrc (yes/no).
644
+ tlrc_opts_at: Specify extra options for @auto_tlrc.
645
+ volreg_base: Set volreg base string (first/third/last).
646
+ verb: Set verbose level.
647
+ runner: Command runner.
648
+ Returns:
649
+ NamedTuple of outputs (described in `UberSubjectPyOutputs`).
650
+ """
651
+ runner = runner or get_global_runner()
652
+ execution = runner.start_execution(UBER_SUBJECT_PY_METADATA)
653
+ params = uber_subject_py_params(
654
+ qt_opts=qt_opts,
655
+ svar=svar,
656
+ cvar=cvar,
657
+ no_gui=no_gui,
658
+ print_ap_command=print_ap_command,
659
+ save_ap_command=save_ap_command,
660
+ exec_ap_command=exec_ap_command,
661
+ exec_proc_script=exec_proc_script,
662
+ align_cost=align_cost,
663
+ align_giant_move=align_giant_move,
664
+ align_opts_aea=align_opts_aea,
665
+ anal_domain=anal_domain,
666
+ anal_type=anal_type,
667
+ anat=anat,
668
+ anat_has_skull=anat_has_skull,
669
+ blocks=blocks,
670
+ blur_size=blur_size,
671
+ epi=epi,
672
+ epi_wildcard=epi_wildcard,
673
+ gid=gid,
674
+ gltsym=gltsym,
675
+ gltsym_label=gltsym_label,
676
+ motion_limit=motion_limit,
677
+ outlier_limit=outlier_limit,
678
+ regress_goforit=regress_goforit,
679
+ regress_bandpass=regress_bandpass,
680
+ regress_jobs=regress_jobs,
681
+ regress_mot_deriv=regress_mot_deriv,
682
+ regress_opts_3d_d=regress_opts_3d_d,
683
+ reml_exec=reml_exec,
684
+ run_clustsim=run_clustsim,
685
+ sid=sid,
686
+ stim=stim,
687
+ stim_basis=stim_basis,
688
+ stim_label=stim_label,
689
+ stim_type=stim_type,
690
+ stim_wildcard=stim_wildcard,
691
+ tcat_nfirst=tcat_nfirst,
692
+ tlrc_base=tlrc_base,
693
+ tlrc_ok_maxite=tlrc_ok_maxite,
694
+ tlrc_opts_at=tlrc_opts_at,
695
+ volreg_base=volreg_base,
696
+ verb=verb,
697
+ )
698
+ return uber_subject_py_execute(params, execution)
699
+
700
+
701
+ __all__ = [
702
+ "UBER_SUBJECT_PY_METADATA",
703
+ "UberSubjectPyOutputs",
704
+ "UberSubjectPyParameters",
705
+ "uber_subject_py",
706
+ "uber_subject_py_params",
707
+ ]