niwrap-afni 0.5.0__py3-none-any.whl
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- niwrap_afni/afni/__init__.py +582 -0
- niwrap_afni/afni/abids_json_info_py.py +247 -0
- niwrap_afni/afni/abids_json_tool_py.py +212 -0
- niwrap_afni/afni/abids_tool.py +191 -0
- niwrap_afni/afni/adjunct_apqc_tsnr_general.py +447 -0
- niwrap_afni/afni/adjunct_aw_tableize_roi_info_py.py +224 -0
- niwrap_afni/afni/adjunct_calc_mont_dims_py.py +173 -0
- niwrap_afni/afni/adjunct_combine_str_py.py +198 -0
- niwrap_afni/afni/adjunct_is_label_py.py +180 -0
- niwrap_afni/afni/adjunct_make_script_and_rst_py.py +237 -0
- niwrap_afni/afni/adjunct_select_str_py.py +188 -0
- niwrap_afni/afni/adjunct_simplify_cost.py +172 -0
- niwrap_afni/afni/adjunct_suma_fs_mask_and_qc.py +249 -0
- niwrap_afni/afni/adjunct_suma_fs_roi_info.py +228 -0
- niwrap_afni/afni/adjunct_tort_plot_dp_align.py +248 -0
- niwrap_afni/afni/adwarp.py +296 -0
- niwrap_afni/afni/afni.py +428 -0
- niwrap_afni/afni/afni_batch_r.py +215 -0
- niwrap_afni/afni/afni_check_omp.py +174 -0
- niwrap_afni/afni/afni_history.py +413 -0
- niwrap_afni/afni/afni_open.py +304 -0
- niwrap_afni/afni/afni_proc_py.py +283 -0
- niwrap_afni/afni/afni_run_r.py +180 -0
- niwrap_afni/afni/afni_system_check_py.py +274 -0
- niwrap_afni/afni/aiv.py +231 -0
- niwrap_afni/afni/align_epi_anat.py +356 -0
- niwrap_afni/afni/analyze_trace.py +292 -0
- niwrap_afni/afni/ap_run_simple_rest.py +293 -0
- niwrap_afni/afni/apqc_make_html.py +175 -0
- niwrap_afni/afni/apqc_make_tcsh_py.py +245 -0
- niwrap_afni/afni/apsearch.py +195 -0
- niwrap_afni/afni/auto_warp_py.py +527 -0
- niwrap_afni/afni/balloon.py +210 -0
- niwrap_afni/afni/bayes_view.py +196 -0
- niwrap_afni/afni/bayesian_group_ana_py.py +342 -0
- niwrap_afni/afni/brain_skin.py +358 -0
- niwrap_afni/afni/build_afni_py.py +330 -0
- niwrap_afni/afni/cat_matvec.py +185 -0
- niwrap_afni/afni/ccalc.py +192 -0
- niwrap_afni/afni/cifti_tool.py +271 -0
- niwrap_afni/afni/cjpeg.py +233 -0
- niwrap_afni/afni/clust_exp_hist_table_py.py +218 -0
- niwrap_afni/afni/clust_exp_stat_parse_py.py +346 -0
- niwrap_afni/afni/column_cat.py +208 -0
- niwrap_afni/afni/compare_surfaces.py +344 -0
- niwrap_afni/afni/convert_cdiflist_to_grads.py +251 -0
- niwrap_afni/afni/convert_dset.py +421 -0
- niwrap_afni/afni/convert_surface.py +247 -0
- niwrap_afni/afni/convex_hull.py +386 -0
- niwrap_afni/afni/count.py +327 -0
- niwrap_afni/afni/create_icosahedron.py +282 -0
- niwrap_afni/afni/dcm2niix_afni.py +550 -0
- niwrap_afni/afni/dicom_hdr.py +263 -0
- niwrap_afni/afni/dicom_hinfo.py +220 -0
- niwrap_afni/afni/dicom_to_raw.py +176 -0
- niwrap_afni/afni/dimon.py +286 -0
- niwrap_afni/afni/djpeg.py +233 -0
- niwrap_afni/afni/drive_suma.py +520 -0
- niwrap_afni/afni/dsetstat2p.py +218 -0
- niwrap_afni/afni/dtistudio_fiberto_segments.py +198 -0
- niwrap_afni/afni/epi_b0_correct.py +485 -0
- niwrap_afni/afni/examine_xmat.py +280 -0
- niwrap_afni/afni/fat_mat2d_plot_py.py +428 -0
- niwrap_afni/afni/fat_mat_sel_py.py +469 -0
- niwrap_afni/afni/fat_mat_tableize.py +292 -0
- niwrap_afni/afni/fat_mvm_gridconv_py.py +207 -0
- niwrap_afni/afni/fat_mvm_prep.py +256 -0
- niwrap_afni/afni/fat_mvm_scripter_py.py +353 -0
- niwrap_afni/afni/fat_proc_align_anat_pair.py +307 -0
- niwrap_afni/afni/fat_proc_axialize_anat.py +415 -0
- niwrap_afni/afni/fat_proc_connec_vis.py +346 -0
- niwrap_afni/afni/fat_proc_convert_dcm_anat.py +283 -0
- niwrap_afni/afni/fat_proc_convert_dcm_dwis.py +374 -0
- niwrap_afni/afni/fat_proc_decmap.py +321 -0
- niwrap_afni/afni/fat_proc_dwi_to_dt.py +522 -0
- niwrap_afni/afni/fat_proc_filter_dwis.py +321 -0
- niwrap_afni/afni/fat_proc_imit2w_from_t1w.py +283 -0
- niwrap_afni/afni/fat_proc_map_to_dti.py +308 -0
- niwrap_afni/afni/fat_proc_select_vols.py +266 -0
- niwrap_afni/afni/fat_roi_row.py +233 -0
- niwrap_afni/afni/fatcat_matplot.py +181 -0
- niwrap_afni/afni/fdrval.py +241 -0
- niwrap_afni/afni/fftest.py +197 -0
- niwrap_afni/afni/file_tool.py +580 -0
- niwrap_afni/afni/fim2.py +465 -0
- niwrap_afni/afni/find_variance_lines.py +353 -0
- niwrap_afni/afni/firdesign.py +235 -0
- niwrap_afni/afni/float_scan.py +213 -0
- niwrap_afni/afni/from3d.py +292 -0
- niwrap_afni/afni/fsread_annot.py +322 -0
- niwrap_afni/afni/gen_epi_review_py.py +292 -0
- niwrap_afni/afni/gen_group_command.py +324 -0
- niwrap_afni/afni/gen_ss_review_scripts.py +421 -0
- niwrap_afni/afni/gen_ss_review_table_py.py +324 -0
- niwrap_afni/afni/get_afni_model_prf.py +196 -0
- niwrap_afni/afni/get_afni_model_prf_6.py +222 -0
- niwrap_afni/afni/get_afni_model_prf_6_bad.py +212 -0
- niwrap_afni/afni/gifti_tool.py +426 -0
- niwrap_afni/afni/gltsymtest.py +193 -0
- niwrap_afni/afni/help_format.py +176 -0
- niwrap_afni/afni/im2niml.py +178 -0
- niwrap_afni/afni/images_equal.py +195 -0
- niwrap_afni/afni/imand.py +203 -0
- niwrap_afni/afni/imaver.py +201 -0
- niwrap_afni/afni/imcalc.py +235 -0
- niwrap_afni/afni/imcat.py +498 -0
- niwrap_afni/afni/imcutup.py +241 -0
- niwrap_afni/afni/imdump.py +177 -0
- niwrap_afni/afni/immask.py +223 -0
- niwrap_afni/afni/imreg.py +389 -0
- niwrap_afni/afni/imrotate.py +217 -0
- niwrap_afni/afni/imstack.py +209 -0
- niwrap_afni/afni/imstat.py +217 -0
- niwrap_afni/afni/imupsam.py +205 -0
- niwrap_afni/afni/init_user_dotfiles_py.py +353 -0
- niwrap_afni/afni/inspec.py +255 -0
- niwrap_afni/afni/iso_surface.py +344 -0
- niwrap_afni/afni/make_color_map.py +417 -0
- niwrap_afni/afni/make_pq_script_py.py +200 -0
- niwrap_afni/afni/make_random_timing_py.py +471 -0
- niwrap_afni/afni/make_stim_times_py.py +304 -0
- niwrap_afni/afni/map_icosahedron.py +296 -0
- niwrap_afni/afni/map_track_id.py +254 -0
- niwrap_afni/afni/mba.py +360 -0
- niwrap_afni/afni/meica_py.py +259 -0
- niwrap_afni/afni/myget.py +186 -0
- niwrap_afni/afni/neuro_deconvolve_py.py +291 -0
- niwrap_afni/afni/nicat.py +207 -0
- niwrap_afni/afni/niccc.py +307 -0
- niwrap_afni/afni/nifti_tool.py +310 -0
- niwrap_afni/afni/niml_feedme.py +260 -0
- niwrap_afni/afni/nsize.py +184 -0
- niwrap_afni/afni/p2dsetstat.py +216 -0
- niwrap_afni/afni/parse_fs_lt_log_py.py +217 -0
- niwrap_afni/afni/plugout_drive.py +259 -0
- niwrap_afni/afni/plugout_ijk.py +297 -0
- niwrap_afni/afni/plugout_tt.py +326 -0
- niwrap_afni/afni/plugout_tta.py +290 -0
- niwrap_afni/afni/prompt_popup.py +205 -0
- niwrap_afni/afni/prompt_user.py +190 -0
- niwrap_afni/afni/pta.py +279 -0
- niwrap_afni/afni/qdelaunay.py +534 -0
- niwrap_afni/afni/qhull.py +376 -0
- niwrap_afni/afni/quick_alpha_vals_py.py +189 -0
- niwrap_afni/afni/quickspec.py +259 -0
- niwrap_afni/afni/quickspec_sl.py +282 -0
- niwrap_afni/afni/quotize.py +194 -0
- niwrap_afni/afni/r_pkgs_install.py +227 -0
- niwrap_afni/afni/rba.py +508 -0
- niwrap_afni/afni/rbox.py +245 -0
- niwrap_afni/afni/read_matlab_files_py.py +225 -0
- niwrap_afni/afni/realtime_receiver.py +310 -0
- niwrap_afni/afni/retro_ts_py.py +477 -0
- niwrap_afni/afni/rmz.py +203 -0
- niwrap_afni/afni/roi2dataset.py +310 -0
- niwrap_afni/afni/roigrow.py +276 -0
- niwrap_afni/afni/rotcom.py +190 -0
- niwrap_afni/afni/rsfgen.py +330 -0
- niwrap_afni/afni/rtfeedme.py +308 -0
- niwrap_afni/afni/samp_bias.py +245 -0
- niwrap_afni/afni/scale_to_map.py +481 -0
- niwrap_afni/afni/serial_helper.py +298 -0
- niwrap_afni/afni/sfim.py +229 -0
- niwrap_afni/afni/slow_surf_clustsim_py.py +285 -0
- niwrap_afni/afni/spharm_deco.py +284 -0
- niwrap_afni/afni/spharm_reco.py +274 -0
- niwrap_afni/afni/stimband.py +229 -0
- niwrap_afni/afni/strblast.py +239 -0
- niwrap_afni/afni/suma_change_spec.py +225 -0
- niwrap_afni/afni/suma_glxdino.py +175 -0
- niwrap_afni/afni/surf2_vol_coord.py +305 -0
- niwrap_afni/afni/surf_clust.py +611 -0
- niwrap_afni/afni/surf_dist.py +208 -0
- niwrap_afni/afni/surf_dset_info.py +355 -0
- niwrap_afni/afni/surf_extrema.py +279 -0
- niwrap_afni/afni/surf_fwhm.py +350 -0
- niwrap_afni/afni/surf_info.py +288 -0
- niwrap_afni/afni/surf_layers.py +300 -0
- niwrap_afni/afni/surf_localstat.py +242 -0
- niwrap_afni/afni/surf_measures.py +373 -0
- niwrap_afni/afni/surf_mesh.py +256 -0
- niwrap_afni/afni/surf_patch.py +412 -0
- niwrap_afni/afni/surf_qual.py +250 -0
- niwrap_afni/afni/surf_retino_map.py +225 -0
- niwrap_afni/afni/surf_smooth.py +388 -0
- niwrap_afni/afni/surf_to_surf.py +327 -0
- niwrap_afni/afni/surface_metrics.py +377 -0
- niwrap_afni/afni/tedana_wrapper_py.py +306 -0
- niwrap_afni/afni/tfim.py +267 -0
- niwrap_afni/afni/timing_tool_py.py +406 -0
- niwrap_afni/afni/to3d.py +643 -0
- niwrap_afni/afni/tokens.py +192 -0
- niwrap_afni/afni/trr.py +405 -0
- niwrap_afni/afni/uber_align_test_py.py +266 -0
- niwrap_afni/afni/uber_proc_py.py +176 -0
- niwrap_afni/afni/uber_skel.py +277 -0
- niwrap_afni/afni/uber_subject_py.py +707 -0
- niwrap_afni/afni/un_warp_epi_py.py +232 -0
- niwrap_afni/afni/uniq_images.py +180 -0
- niwrap_afni/afni/v_1d_apar2mat.py +262 -0
- niwrap_afni/afni/v_1d_astrip.py +176 -0
- niwrap_afni/afni/v_1d_bandpass.py +238 -0
- niwrap_afni/afni/v_1d_bport.py +277 -0
- niwrap_afni/afni/v_1d_correlate.py +218 -0
- niwrap_afni/afni/v_1d_dw_grad_o_mat__.py +429 -0
- niwrap_afni/afni/v_1d_flag_motion.py +212 -0
- niwrap_afni/afni/v_1d_marry.py +214 -0
- niwrap_afni/afni/v_1d_nlfit.py +254 -0
- niwrap_afni/afni/v_1d_rplot.py +180 -0
- niwrap_afni/afni/v_1d_sem.py +215 -0
- niwrap_afni/afni/v_1d_tool_py.py +319 -0
- niwrap_afni/afni/v_1d_tsort.py +216 -0
- niwrap_afni/afni/v_1d_upsample.py +195 -0
- niwrap_afni/afni/v_1dcat.py +266 -0
- niwrap_afni/afni/v_1ddot.py +249 -0
- niwrap_afni/afni/v_1deval.py +265 -0
- niwrap_afni/afni/v_1dfft.py +269 -0
- niwrap_afni/afni/v_1dgen_arma11.py +319 -0
- niwrap_afni/afni/v_1dgrayplot.py +238 -0
- niwrap_afni/afni/v_1dmatcalc.py +180 -0
- niwrap_afni/afni/v_1dnorm.py +224 -0
- niwrap_afni/afni/v_1dplot.py +831 -0
- niwrap_afni/afni/v_1dplot_py.py +578 -0
- niwrap_afni/afni/v_1dsound.py +292 -0
- niwrap_afni/afni/v_1dsum.py +235 -0
- niwrap_afni/afni/v_1dsvd.py +272 -0
- niwrap_afni/afni/v_1dtranspose.py +188 -0
- niwrap_afni/afni/v_24swap.py +194 -0
- niwrap_afni/afni/v_2d_im_reg.py +312 -0
- niwrap_afni/afni/v_2dcat.py +496 -0
- niwrap_afni/afni/v_2perm.py +233 -0
- niwrap_afni/afni/v_2swap.py +181 -0
- niwrap_afni/afni/v_3_droimaker.py +419 -0
- niwrap_afni/afni/v_3d_aboverlap.py +211 -0
- niwrap_afni/afni/v_3d_acost.py +210 -0
- niwrap_afni/afni/v_3d_afnito3_d.py +177 -0
- niwrap_afni/afni/v_3d_afnito_analyze.py +219 -0
- niwrap_afni/afni/v_3d_afnito_nifti.py +245 -0
- niwrap_afni/afni/v_3d_afnito_niml.py +175 -0
- niwrap_afni/afni/v_3d_afnito_raw.py +202 -0
- niwrap_afni/afni/v_3d_allineate.py +350 -0
- niwrap_afni/afni/v_3d_amp_to_rsfc.py +262 -0
- niwrap_afni/afni/v_3d_anhist.py +260 -0
- niwrap_afni/afni/v_3d_anova.py +359 -0
- niwrap_afni/afni/v_3d_anova2.py +515 -0
- niwrap_afni/afni/v_3d_anova3.py +302 -0
- niwrap_afni/afni/v_3d_attribute.py +248 -0
- niwrap_afni/afni/v_3d_auto_tcorrelate.py +314 -0
- niwrap_afni/afni/v_3d_autobox.py +335 -0
- niwrap_afni/afni/v_3d_automask.py +258 -0
- niwrap_afni/afni/v_3d_ball_match.py +229 -0
- niwrap_afni/afni/v_3d_bandpass.py +381 -0
- niwrap_afni/afni/v_3d_blur_in_mask.py +291 -0
- niwrap_afni/afni/v_3d_blur_to_fwhm.py +267 -0
- niwrap_afni/afni/v_3d_brain_sync.py +267 -0
- niwrap_afni/afni/v_3d_brain_voyagerto_afni.py +313 -0
- niwrap_afni/afni/v_3d_brick_stat.py +463 -0
- niwrap_afni/afni/v_3d_clip_level.py +175 -0
- niwrap_afni/afni/v_3d_clust_count.py +229 -0
- niwrap_afni/afni/v_3d_clust_sim.py +196 -0
- niwrap_afni/afni/v_3d_clusterize.py +448 -0
- niwrap_afni/afni/v_3d_cm.py +177 -0
- niwrap_afni/afni/v_3d_compare_affine.py +215 -0
- niwrap_afni/afni/v_3d_conformist.py +176 -0
- niwrap_afni/afni/v_3d_convolve.py +197 -0
- niwrap_afni/afni/v_3d_cruiseto_afni.py +264 -0
- niwrap_afni/afni/v_3d_deconvolve.py +371 -0
- niwrap_afni/afni/v_3d_degree_centrality.py +270 -0
- niwrap_afni/afni/v_3d_depth_map.py +317 -0
- niwrap_afni/afni/v_3d_despike.py +191 -0
- niwrap_afni/afni/v_3d_detrend.py +191 -0
- niwrap_afni/afni/v_3d_dft.py +245 -0
- niwrap_afni/afni/v_3d_diff.py +254 -0
- niwrap_afni/afni/v_3d_dteig.py +236 -0
- niwrap_afni/afni/v_3d_dtto_dwi.py +199 -0
- niwrap_afni/afni/v_3d_dtto_noisy_dwi.py +275 -0
- niwrap_afni/afni/v_3d_dwito_dt.py +191 -0
- niwrap_afni/afni/v_3d_dwuncert.py +283 -0
- niwrap_afni/afni/v_3d_ecm.py +363 -0
- niwrap_afni/afni/v_3d_edu_01_scale.py +216 -0
- niwrap_afni/afni/v_3d_eigs_to_dt.py +271 -0
- niwrap_afni/afni/v_3d_empty.py +224 -0
- niwrap_afni/afni/v_3d_entropy.py +181 -0
- niwrap_afni/afni/v_3d_errts_cormat.py +243 -0
- niwrap_afni/afni/v_3d_exchange.py +226 -0
- niwrap_afni/afni/v_3d_extract_group_in_corr.py +195 -0
- niwrap_afni/afni/v_3d_extrema.py +384 -0
- niwrap_afni/afni/v_3d_fdr.py +325 -0
- niwrap_afni/afni/v_3d_fft.py +307 -0
- niwrap_afni/afni/v_3d_friedman.py +226 -0
- niwrap_afni/afni/v_3d_fwhmx.py +321 -0
- niwrap_afni/afni/v_3d_gen_feature_dist.py +262 -0
- niwrap_afni/afni/v_3d_gen_priors.py +487 -0
- niwrap_afni/afni/v_3d_getrow.py +243 -0
- niwrap_afni/afni/v_3d_grayplot.py +343 -0
- niwrap_afni/afni/v_3d_group_in_corr.py +484 -0
- niwrap_afni/afni/v_3d_hist.py +406 -0
- niwrap_afni/afni/v_3d_icc.py +228 -0
- niwrap_afni/afni/v_3d_intracranial.py +275 -0
- niwrap_afni/afni/v_3d_inv_fmri.py +317 -0
- niwrap_afni/afni/v_3d_isc.py +298 -0
- niwrap_afni/afni/v_3d_kruskal_wallis.py +231 -0
- niwrap_afni/afni/v_3d_lfcd.py +249 -0
- niwrap_afni/afni/v_3d_lme.py +524 -0
- niwrap_afni/afni/v_3d_lmer.py +425 -0
- niwrap_afni/afni/v_3d_local_acf.py +224 -0
- niwrap_afni/afni/v_3d_local_bistat.py +325 -0
- niwrap_afni/afni/v_3d_local_histog.py +268 -0
- niwrap_afni/afni/v_3d_local_pv.py +318 -0
- niwrap_afni/afni/v_3d_local_svd.py +258 -0
- niwrap_afni/afni/v_3d_local_unifize.py +286 -0
- niwrap_afni/afni/v_3d_localstat.py +427 -0
- niwrap_afni/afni/v_3d_lomb_scargle.py +307 -0
- niwrap_afni/afni/v_3d_lrflip.py +202 -0
- niwrap_afni/afni/v_3d_lss.py +175 -0
- niwrap_afni/afni/v_3d_mann_whitney.py +234 -0
- niwrap_afni/afni/v_3d_mask_to_ascii.py +189 -0
- niwrap_afni/afni/v_3d_match.py +300 -0
- niwrap_afni/afni/v_3d_mean.py +364 -0
- niwrap_afni/afni/v_3d_median_filter.py +238 -0
- niwrap_afni/afni/v_3d_mema.py +171 -0
- niwrap_afni/afni/v_3d_mepfm.py +256 -0
- niwrap_afni/afni/v_3d_mse.py +283 -0
- niwrap_afni/afni/v_3d_mss.py +397 -0
- niwrap_afni/afni/v_3d_multi_thresh.py +306 -0
- niwrap_afni/afni/v_3d_mvm.py +359 -0
- niwrap_afni/afni/v_3d_mvm_validator.py +191 -0
- niwrap_afni/afni/v_3d_net_corr.py +398 -0
- niwrap_afni/afni/v_3d_nlfim.py +241 -0
- niwrap_afni/afni/v_3d_normality_test.py +209 -0
- niwrap_afni/afni/v_3d_notes.py +246 -0
- niwrap_afni/afni/v_3d_nwarp_adjust.py +218 -0
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V_3D_TSTAT_METADATA = Metadata(
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id="2c3351f9c202b2f87198789eb63df2ff52ca3826.boutiques",
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+
Get build cargs function by command type.
|
|
86
|
+
|
|
87
|
+
Args:
|
|
88
|
+
t: Command type.
|
|
89
|
+
Returns:
|
|
90
|
+
Build cargs function.
|
|
91
|
+
"""
|
|
92
|
+
return {
|
|
93
|
+
"3dTstat": v_3d_tstat_cargs,
|
|
94
|
+
}.get(t)
|
|
95
|
+
|
|
96
|
+
|
|
97
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+
def dyn_outputs(
|
|
98
|
+
t: str,
|
|
99
|
+
) -> typing.Any:
|
|
100
|
+
"""
|
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101
|
+
Get build outputs function by command type.
|
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102
|
+
|
|
103
|
+
Args:
|
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104
|
+
t: Command type.
|
|
105
|
+
Returns:
|
|
106
|
+
Build outputs function.
|
|
107
|
+
"""
|
|
108
|
+
return {
|
|
109
|
+
"3dTstat": v_3d_tstat_outputs,
|
|
110
|
+
}.get(t)
|
|
111
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+
|
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112
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+
|
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113
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+
class V3dTstatOutputs(typing.NamedTuple):
|
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114
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+
"""
|
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115
|
+
Output object returned when calling `v_3d_tstat(...)`.
|
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116
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+
"""
|
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+
root: OutputPathType
|
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118
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+
"""Output root folder. This is the root folder for all outputs."""
|
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+
out_file: OutputPathType | None
|
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120
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+
"""Output image file name."""
|
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121
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+
|
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122
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+
|
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123
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+
def v_3d_tstat_params(
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+
in_file: InputPathType,
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+
mask: InputPathType | None = None,
|
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126
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+
num_threads: int | None = None,
|
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127
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+
sum_: bool = False,
|
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128
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+
abssum: bool = False,
|
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129
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+
sos: bool = False,
|
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130
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+
l2norm: bool = False,
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131
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+
mean: bool = False,
|
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132
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+
slope: bool = False,
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133
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+
stdev: bool = False,
|
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134
|
+
stdev_nod: bool = False,
|
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135
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+
cvar: bool = False,
|
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136
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+
cvar_nod: bool = False,
|
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137
|
+
cvarinv: bool = False,
|
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138
|
+
cvarinv_nod: bool = False,
|
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139
|
+
tsnr: bool = False,
|
|
140
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+
mad: bool = False,
|
|
141
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+
dw: bool = False,
|
|
142
|
+
median: bool = False,
|
|
143
|
+
nzmedian: bool = False,
|
|
144
|
+
nzstdev: bool = False,
|
|
145
|
+
bmv: bool = False,
|
|
146
|
+
mssd: bool = False,
|
|
147
|
+
mssdsqrt: bool = False,
|
|
148
|
+
masdx: bool = False,
|
|
149
|
+
min_: bool = False,
|
|
150
|
+
max_: bool = False,
|
|
151
|
+
absmax: bool = False,
|
|
152
|
+
signed_absmax: bool = False,
|
|
153
|
+
percentile: bool = False,
|
|
154
|
+
argmin: bool = False,
|
|
155
|
+
argmin1: bool = False,
|
|
156
|
+
argmax: bool = False,
|
|
157
|
+
argmax1: bool = False,
|
|
158
|
+
argabsmax: bool = False,
|
|
159
|
+
argabsmax1: bool = False,
|
|
160
|
+
duration: bool = False,
|
|
161
|
+
onset: bool = False,
|
|
162
|
+
offset: bool = False,
|
|
163
|
+
centroid: bool = False,
|
|
164
|
+
centduration: bool = False,
|
|
165
|
+
nzmean: bool = False,
|
|
166
|
+
zcount: bool = False,
|
|
167
|
+
nzcount: bool = False,
|
|
168
|
+
autocorr: bool = False,
|
|
169
|
+
autoreg: bool = False,
|
|
170
|
+
accumulate: bool = False,
|
|
171
|
+
centromean: bool = False,
|
|
172
|
+
skewness: bool = False,
|
|
173
|
+
kurtosis: bool = False,
|
|
174
|
+
firstvalue: bool = False,
|
|
175
|
+
tdiff: bool = False,
|
|
176
|
+
prefix: str | None = None,
|
|
177
|
+
datum: str | None = None,
|
|
178
|
+
nscale: bool = False,
|
|
179
|
+
basepercent: float | None = None,
|
|
180
|
+
mask_mset: InputPathType | None = None,
|
|
181
|
+
mrange: str | None = None,
|
|
182
|
+
cmask: str | None = None,
|
|
183
|
+
outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
|
|
184
|
+
) -> V3dTstatParameters:
|
|
185
|
+
"""
|
|
186
|
+
Build parameters.
|
|
187
|
+
|
|
188
|
+
Args:
|
|
189
|
+
in_file: Input file to 3dtstat.
|
|
190
|
+
mask: Mask file.
|
|
191
|
+
num_threads: Set number of threads.
|
|
192
|
+
sum_: Compute sum of input voxels.
|
|
193
|
+
abssum: Compute absolute sum of input voxels.
|
|
194
|
+
sos: Compute sum of squares.
|
|
195
|
+
l2norm: Compute L2 norm (sqrt(sum squares)).
|
|
196
|
+
mean: Compute mean of input voxels.
|
|
197
|
+
slope: Compute the slope of input voxels vs. time.
|
|
198
|
+
stdev: Compute standard deviation of input voxels.
|
|
199
|
+
stdev_nod: Compute standard deviation of input voxels without\
|
|
200
|
+
detrending.
|
|
201
|
+
cvar: Compute coefficient of variation of input voxels.
|
|
202
|
+
cvar_nod: Compute coefficient of variation of input voxels without\
|
|
203
|
+
detrending.
|
|
204
|
+
cvarinv: Compute inverse coefficient of variation of input voxels.
|
|
205
|
+
cvarinv_nod: Compute inverse coefficient of variation of input voxels\
|
|
206
|
+
without detrending.
|
|
207
|
+
tsnr: Compute temporal signal to noise ratio.
|
|
208
|
+
mad: Compute median absolute deviation of input voxels.
|
|
209
|
+
dw: Compute Durbin-Watson Statistic of input voxels.
|
|
210
|
+
median: Compute median of input voxels.
|
|
211
|
+
nzmedian: Compute median of non-zero input voxels.
|
|
212
|
+
nzstdev: Compute standard deviation of non-zero input voxels.
|
|
213
|
+
bmv: Compute biweight midvariance of input voxels.
|
|
214
|
+
mssd: Compute mean of successive squared differences of input voxels.
|
|
215
|
+
mssdsqrt: Compute square root of mean of successive squared differences\
|
|
216
|
+
of input voxels.
|
|
217
|
+
masdx: Compute median of absolute values of first time differences of\
|
|
218
|
+
input voxels.
|
|
219
|
+
min_: Compute minimum of input voxels.
|
|
220
|
+
max_: Compute maximum of input voxels.
|
|
221
|
+
absmax: Compute absolute maximum of input voxels.
|
|
222
|
+
signed_absmax: Compute signed absolute maximum of input voxels.
|
|
223
|
+
percentile: Compute the P-th percentile point of the data in each voxel\
|
|
224
|
+
time series.
|
|
225
|
+
argmin: Compute index of minimum of input voxels.
|
|
226
|
+
argmin1: Compute index + 1 of minimum of input voxels.
|
|
227
|
+
argmax: Compute index of maximum of input voxels.
|
|
228
|
+
argmax1: Compute index + 1 of maximum of input voxels.
|
|
229
|
+
argabsmax: Compute index of absolute maximum of input voxels.
|
|
230
|
+
argabsmax1: Compute index + 1 of absolute maximum of input voxels.
|
|
231
|
+
duration: Compute number of points around max above a threshold.
|
|
232
|
+
onset: Compute beginning of duration around max where value exceeds\
|
|
233
|
+
basepercent.
|
|
234
|
+
offset: Compute end of duration around max where value exceeds\
|
|
235
|
+
basepercent.
|
|
236
|
+
centroid: Compute centroid of data time curves.
|
|
237
|
+
centduration: Compute duration using centroid's index as center.
|
|
238
|
+
nzmean: Compute mean of non-zero voxels.
|
|
239
|
+
zcount: Count number of zero values at each voxel.
|
|
240
|
+
nzcount: Count number of non-zero values at each voxel.
|
|
241
|
+
autocorr: Compute autocorrelation function and return first n\
|
|
242
|
+
coefficients.
|
|
243
|
+
autoreg: Compute autoregression coefficients and return first n\
|
|
244
|
+
coefficients.
|
|
245
|
+
accumulate: Accumulate time series values (partial sums).
|
|
246
|
+
centromean: Compute mean of middle 50% of voxel values.
|
|
247
|
+
skewness: Measure of asymmetry in distribution.
|
|
248
|
+
kurtosis: Measure of the 'tailedness' of the probability distribution.
|
|
249
|
+
firstvalue: First value in dataset.
|
|
250
|
+
tdiff: Take the first difference of each time series before further\
|
|
251
|
+
processing.
|
|
252
|
+
prefix: Use string 'p' for the prefix of the output dataset [DEFAULT =\
|
|
253
|
+
'stat'].
|
|
254
|
+
datum: Use data type 'd' for the type of storage of the output, where\
|
|
255
|
+
'd' is one of 'byte', 'short', or 'float' [DEFAULT=float].
|
|
256
|
+
nscale: Do not scale output values when datum is byte or short. Scaling\
|
|
257
|
+
is done by default.
|
|
258
|
+
basepercent: Percentage of maximum for duration calculation.
|
|
259
|
+
mask_mset: Use the dataset 'mset' as a mask. Only voxels with nonzero\
|
|
260
|
+
values in 'mset' will be printed from 'dataset'.
|
|
261
|
+
mrange: Further restrict the voxels from 'mset' so that only those mask\
|
|
262
|
+
values between 'a' and 'b' (inclusive) will be used.
|
|
263
|
+
cmask: Execute the options enclosed in single quotes as a 3dcalc-like\
|
|
264
|
+
program, and produce a mask from the resulting 3D brick.
|
|
265
|
+
outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
|
|
266
|
+
Returns:
|
|
267
|
+
Parameter dictionary
|
|
268
|
+
"""
|
|
269
|
+
params = {
|
|
270
|
+
"__STYXTYPE__": "3dTstat",
|
|
271
|
+
"sum": sum_,
|
|
272
|
+
"abssum": abssum,
|
|
273
|
+
"sos": sos,
|
|
274
|
+
"l2norm": l2norm,
|
|
275
|
+
"mean": mean,
|
|
276
|
+
"slope": slope,
|
|
277
|
+
"stdev": stdev,
|
|
278
|
+
"stdevNOD": stdev_nod,
|
|
279
|
+
"cvar": cvar,
|
|
280
|
+
"cvarNOD": cvar_nod,
|
|
281
|
+
"cvarinv": cvarinv,
|
|
282
|
+
"cvarinvNOD": cvarinv_nod,
|
|
283
|
+
"tsnr": tsnr,
|
|
284
|
+
"MAD": mad,
|
|
285
|
+
"DW": dw,
|
|
286
|
+
"median": median,
|
|
287
|
+
"nzmedian": nzmedian,
|
|
288
|
+
"nzstdev": nzstdev,
|
|
289
|
+
"bmv": bmv,
|
|
290
|
+
"MSSD": mssd,
|
|
291
|
+
"MSSDsqrt": mssdsqrt,
|
|
292
|
+
"MASDx": masdx,
|
|
293
|
+
"min": min_,
|
|
294
|
+
"max": max_,
|
|
295
|
+
"absmax": absmax,
|
|
296
|
+
"signed_absmax": signed_absmax,
|
|
297
|
+
"percentile": percentile,
|
|
298
|
+
"argmin": argmin,
|
|
299
|
+
"argmin1": argmin1,
|
|
300
|
+
"argmax": argmax,
|
|
301
|
+
"argmax1": argmax1,
|
|
302
|
+
"argabsmax": argabsmax,
|
|
303
|
+
"argabsmax1": argabsmax1,
|
|
304
|
+
"duration": duration,
|
|
305
|
+
"onset": onset,
|
|
306
|
+
"offset": offset,
|
|
307
|
+
"centroid": centroid,
|
|
308
|
+
"centduration": centduration,
|
|
309
|
+
"nzmean": nzmean,
|
|
310
|
+
"zcount": zcount,
|
|
311
|
+
"nzcount": nzcount,
|
|
312
|
+
"autocorr": autocorr,
|
|
313
|
+
"autoreg": autoreg,
|
|
314
|
+
"accumulate": accumulate,
|
|
315
|
+
"centromean": centromean,
|
|
316
|
+
"skewness": skewness,
|
|
317
|
+
"kurtosis": kurtosis,
|
|
318
|
+
"firstvalue": firstvalue,
|
|
319
|
+
"tdiff": tdiff,
|
|
320
|
+
"nscale": nscale,
|
|
321
|
+
"in_file": in_file,
|
|
322
|
+
}
|
|
323
|
+
if mask is not None:
|
|
324
|
+
params["mask"] = mask
|
|
325
|
+
if num_threads is not None:
|
|
326
|
+
params["num_threads"] = num_threads
|
|
327
|
+
if prefix is not None:
|
|
328
|
+
params["prefix"] = prefix
|
|
329
|
+
if datum is not None:
|
|
330
|
+
params["datum"] = datum
|
|
331
|
+
if basepercent is not None:
|
|
332
|
+
params["basepercent"] = basepercent
|
|
333
|
+
if mask_mset is not None:
|
|
334
|
+
params["mask_mset"] = mask_mset
|
|
335
|
+
if mrange is not None:
|
|
336
|
+
params["mrange"] = mrange
|
|
337
|
+
if cmask is not None:
|
|
338
|
+
params["cmask"] = cmask
|
|
339
|
+
if outputtype is not None:
|
|
340
|
+
params["outputtype"] = outputtype
|
|
341
|
+
return params
|
|
342
|
+
|
|
343
|
+
|
|
344
|
+
def v_3d_tstat_cargs(
|
|
345
|
+
params: V3dTstatParameters,
|
|
346
|
+
execution: Execution,
|
|
347
|
+
) -> list[str]:
|
|
348
|
+
"""
|
|
349
|
+
Build command-line arguments from parameters.
|
|
350
|
+
|
|
351
|
+
Args:
|
|
352
|
+
params: The parameters.
|
|
353
|
+
execution: The execution object for resolving input paths.
|
|
354
|
+
Returns:
|
|
355
|
+
Command-line arguments.
|
|
356
|
+
"""
|
|
357
|
+
cargs = []
|
|
358
|
+
cargs.append("3dTstat")
|
|
359
|
+
if params.get("mask") is not None:
|
|
360
|
+
cargs.extend([
|
|
361
|
+
"-mask",
|
|
362
|
+
execution.input_file(params.get("mask"))
|
|
363
|
+
])
|
|
364
|
+
if params.get("num_threads") is not None:
|
|
365
|
+
cargs.append(str(params.get("num_threads")))
|
|
366
|
+
if params.get("sum"):
|
|
367
|
+
cargs.append("-sum")
|
|
368
|
+
if params.get("abssum"):
|
|
369
|
+
cargs.append("-abssum")
|
|
370
|
+
if params.get("sos"):
|
|
371
|
+
cargs.append("-sos")
|
|
372
|
+
if params.get("l2norm"):
|
|
373
|
+
cargs.append("-l2norm")
|
|
374
|
+
if params.get("mean"):
|
|
375
|
+
cargs.append("-mean")
|
|
376
|
+
if params.get("slope"):
|
|
377
|
+
cargs.append("-slope")
|
|
378
|
+
if params.get("stdev"):
|
|
379
|
+
cargs.append("-stdev")
|
|
380
|
+
if params.get("stdevNOD"):
|
|
381
|
+
cargs.append("-stdevNOD")
|
|
382
|
+
if params.get("cvar"):
|
|
383
|
+
cargs.append("-cvar")
|
|
384
|
+
if params.get("cvarNOD"):
|
|
385
|
+
cargs.append("-cvarNOD")
|
|
386
|
+
if params.get("cvarinv"):
|
|
387
|
+
cargs.append("-cvarinv")
|
|
388
|
+
if params.get("cvarinvNOD"):
|
|
389
|
+
cargs.append("-cvarinvNOD")
|
|
390
|
+
if params.get("tsnr"):
|
|
391
|
+
cargs.append("-tsnr")
|
|
392
|
+
if params.get("MAD"):
|
|
393
|
+
cargs.append("-MAD")
|
|
394
|
+
if params.get("DW"):
|
|
395
|
+
cargs.append("-DW")
|
|
396
|
+
if params.get("median"):
|
|
397
|
+
cargs.append("-median")
|
|
398
|
+
if params.get("nzmedian"):
|
|
399
|
+
cargs.append("-nzmedian")
|
|
400
|
+
if params.get("nzstdev"):
|
|
401
|
+
cargs.append("-nzstdev")
|
|
402
|
+
if params.get("bmv"):
|
|
403
|
+
cargs.append("-bmv")
|
|
404
|
+
if params.get("MSSD"):
|
|
405
|
+
cargs.append("-MSSD")
|
|
406
|
+
if params.get("MSSDsqrt"):
|
|
407
|
+
cargs.append("-MSSDsqrt")
|
|
408
|
+
if params.get("MASDx"):
|
|
409
|
+
cargs.append("-MASDx")
|
|
410
|
+
if params.get("min"):
|
|
411
|
+
cargs.append("-min")
|
|
412
|
+
if params.get("max"):
|
|
413
|
+
cargs.append("-max")
|
|
414
|
+
if params.get("absmax"):
|
|
415
|
+
cargs.append("-absmax")
|
|
416
|
+
if params.get("signed_absmax"):
|
|
417
|
+
cargs.append("-signed_absmax")
|
|
418
|
+
if params.get("percentile"):
|
|
419
|
+
cargs.append("-percentile")
|
|
420
|
+
if params.get("argmin"):
|
|
421
|
+
cargs.append("-argmin")
|
|
422
|
+
if params.get("argmin1"):
|
|
423
|
+
cargs.append("-argmin1")
|
|
424
|
+
if params.get("argmax"):
|
|
425
|
+
cargs.append("-argmax")
|
|
426
|
+
if params.get("argmax1"):
|
|
427
|
+
cargs.append("-argmax1")
|
|
428
|
+
if params.get("argabsmax"):
|
|
429
|
+
cargs.append("-argabsmax")
|
|
430
|
+
if params.get("argabsmax1"):
|
|
431
|
+
cargs.append("-argabsmax1")
|
|
432
|
+
if params.get("duration"):
|
|
433
|
+
cargs.append("-duration")
|
|
434
|
+
if params.get("onset"):
|
|
435
|
+
cargs.append("-onset")
|
|
436
|
+
if params.get("offset"):
|
|
437
|
+
cargs.append("-offset")
|
|
438
|
+
if params.get("centroid"):
|
|
439
|
+
cargs.append("-centroid")
|
|
440
|
+
if params.get("centduration"):
|
|
441
|
+
cargs.append("-centduration")
|
|
442
|
+
if params.get("nzmean"):
|
|
443
|
+
cargs.append("-nzmean")
|
|
444
|
+
if params.get("zcount"):
|
|
445
|
+
cargs.append("-zcount")
|
|
446
|
+
if params.get("nzcount"):
|
|
447
|
+
cargs.append("-nzcount")
|
|
448
|
+
if params.get("autocorr"):
|
|
449
|
+
cargs.append("-autocorr")
|
|
450
|
+
if params.get("autoreg"):
|
|
451
|
+
cargs.append("-autoreg")
|
|
452
|
+
if params.get("accumulate"):
|
|
453
|
+
cargs.append("-accumulate")
|
|
454
|
+
if params.get("centromean"):
|
|
455
|
+
cargs.append("-centromean")
|
|
456
|
+
if params.get("skewness"):
|
|
457
|
+
cargs.append("-skewness")
|
|
458
|
+
if params.get("kurtosis"):
|
|
459
|
+
cargs.append("-kurtosis")
|
|
460
|
+
if params.get("firstvalue"):
|
|
461
|
+
cargs.append("-firstvalue")
|
|
462
|
+
if params.get("tdiff"):
|
|
463
|
+
cargs.append("-tdiff")
|
|
464
|
+
if params.get("prefix") is not None:
|
|
465
|
+
cargs.extend([
|
|
466
|
+
"-prefix",
|
|
467
|
+
params.get("prefix")
|
|
468
|
+
])
|
|
469
|
+
if params.get("datum") is not None:
|
|
470
|
+
cargs.extend([
|
|
471
|
+
"-datum",
|
|
472
|
+
params.get("datum")
|
|
473
|
+
])
|
|
474
|
+
if params.get("nscale"):
|
|
475
|
+
cargs.append("-nscale")
|
|
476
|
+
if params.get("basepercent") is not None:
|
|
477
|
+
cargs.extend([
|
|
478
|
+
"-basepercent",
|
|
479
|
+
str(params.get("basepercent"))
|
|
480
|
+
])
|
|
481
|
+
if params.get("mask_mset") is not None:
|
|
482
|
+
cargs.extend([
|
|
483
|
+
"-mask",
|
|
484
|
+
execution.input_file(params.get("mask_mset"))
|
|
485
|
+
])
|
|
486
|
+
if params.get("mrange") is not None:
|
|
487
|
+
cargs.extend([
|
|
488
|
+
"-mrange",
|
|
489
|
+
params.get("mrange")
|
|
490
|
+
])
|
|
491
|
+
if params.get("cmask") is not None:
|
|
492
|
+
cargs.extend([
|
|
493
|
+
"-cmask",
|
|
494
|
+
params.get("cmask")
|
|
495
|
+
])
|
|
496
|
+
if params.get("outputtype") is not None:
|
|
497
|
+
cargs.append(params.get("outputtype"))
|
|
498
|
+
cargs.append(execution.input_file(params.get("in_file")))
|
|
499
|
+
return cargs
|
|
500
|
+
|
|
501
|
+
|
|
502
|
+
def v_3d_tstat_outputs(
|
|
503
|
+
params: V3dTstatParameters,
|
|
504
|
+
execution: Execution,
|
|
505
|
+
) -> V3dTstatOutputs:
|
|
506
|
+
"""
|
|
507
|
+
Build outputs object containing output file paths and possibly stdout/stderr.
|
|
508
|
+
|
|
509
|
+
Args:
|
|
510
|
+
params: The parameters.
|
|
511
|
+
execution: The execution object for resolving input paths.
|
|
512
|
+
Returns:
|
|
513
|
+
Outputs object.
|
|
514
|
+
"""
|
|
515
|
+
ret = V3dTstatOutputs(
|
|
516
|
+
root=execution.output_file("."),
|
|
517
|
+
out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
|
|
518
|
+
)
|
|
519
|
+
return ret
|
|
520
|
+
|
|
521
|
+
|
|
522
|
+
def v_3d_tstat_execute(
|
|
523
|
+
params: V3dTstatParameters,
|
|
524
|
+
execution: Execution,
|
|
525
|
+
) -> V3dTstatOutputs:
|
|
526
|
+
"""
|
|
527
|
+
Compute voxel-wise statistics using AFNI 3dTstat command.
|
|
528
|
+
|
|
529
|
+
Author: AFNI Developers
|
|
530
|
+
|
|
531
|
+
URL: https://afni.nimh.nih.gov/
|
|
532
|
+
|
|
533
|
+
Args:
|
|
534
|
+
params: The parameters.
|
|
535
|
+
execution: The execution object.
|
|
536
|
+
Returns:
|
|
537
|
+
NamedTuple of outputs (described in `V3dTstatOutputs`).
|
|
538
|
+
"""
|
|
539
|
+
params = execution.params(params)
|
|
540
|
+
cargs = v_3d_tstat_cargs(params, execution)
|
|
541
|
+
ret = v_3d_tstat_outputs(params, execution)
|
|
542
|
+
execution.run(cargs)
|
|
543
|
+
return ret
|
|
544
|
+
|
|
545
|
+
|
|
546
|
+
def v_3d_tstat(
|
|
547
|
+
in_file: InputPathType,
|
|
548
|
+
mask: InputPathType | None = None,
|
|
549
|
+
num_threads: int | None = None,
|
|
550
|
+
sum_: bool = False,
|
|
551
|
+
abssum: bool = False,
|
|
552
|
+
sos: bool = False,
|
|
553
|
+
l2norm: bool = False,
|
|
554
|
+
mean: bool = False,
|
|
555
|
+
slope: bool = False,
|
|
556
|
+
stdev: bool = False,
|
|
557
|
+
stdev_nod: bool = False,
|
|
558
|
+
cvar: bool = False,
|
|
559
|
+
cvar_nod: bool = False,
|
|
560
|
+
cvarinv: bool = False,
|
|
561
|
+
cvarinv_nod: bool = False,
|
|
562
|
+
tsnr: bool = False,
|
|
563
|
+
mad: bool = False,
|
|
564
|
+
dw: bool = False,
|
|
565
|
+
median: bool = False,
|
|
566
|
+
nzmedian: bool = False,
|
|
567
|
+
nzstdev: bool = False,
|
|
568
|
+
bmv: bool = False,
|
|
569
|
+
mssd: bool = False,
|
|
570
|
+
mssdsqrt: bool = False,
|
|
571
|
+
masdx: bool = False,
|
|
572
|
+
min_: bool = False,
|
|
573
|
+
max_: bool = False,
|
|
574
|
+
absmax: bool = False,
|
|
575
|
+
signed_absmax: bool = False,
|
|
576
|
+
percentile: bool = False,
|
|
577
|
+
argmin: bool = False,
|
|
578
|
+
argmin1: bool = False,
|
|
579
|
+
argmax: bool = False,
|
|
580
|
+
argmax1: bool = False,
|
|
581
|
+
argabsmax: bool = False,
|
|
582
|
+
argabsmax1: bool = False,
|
|
583
|
+
duration: bool = False,
|
|
584
|
+
onset: bool = False,
|
|
585
|
+
offset: bool = False,
|
|
586
|
+
centroid: bool = False,
|
|
587
|
+
centduration: bool = False,
|
|
588
|
+
nzmean: bool = False,
|
|
589
|
+
zcount: bool = False,
|
|
590
|
+
nzcount: bool = False,
|
|
591
|
+
autocorr: bool = False,
|
|
592
|
+
autoreg: bool = False,
|
|
593
|
+
accumulate: bool = False,
|
|
594
|
+
centromean: bool = False,
|
|
595
|
+
skewness: bool = False,
|
|
596
|
+
kurtosis: bool = False,
|
|
597
|
+
firstvalue: bool = False,
|
|
598
|
+
tdiff: bool = False,
|
|
599
|
+
prefix: str | None = None,
|
|
600
|
+
datum: str | None = None,
|
|
601
|
+
nscale: bool = False,
|
|
602
|
+
basepercent: float | None = None,
|
|
603
|
+
mask_mset: InputPathType | None = None,
|
|
604
|
+
mrange: str | None = None,
|
|
605
|
+
cmask: str | None = None,
|
|
606
|
+
outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
|
|
607
|
+
runner: Runner | None = None,
|
|
608
|
+
) -> V3dTstatOutputs:
|
|
609
|
+
"""
|
|
610
|
+
Compute voxel-wise statistics using AFNI 3dTstat command.
|
|
611
|
+
|
|
612
|
+
Author: AFNI Developers
|
|
613
|
+
|
|
614
|
+
URL: https://afni.nimh.nih.gov/
|
|
615
|
+
|
|
616
|
+
Args:
|
|
617
|
+
in_file: Input file to 3dtstat.
|
|
618
|
+
mask: Mask file.
|
|
619
|
+
num_threads: Set number of threads.
|
|
620
|
+
sum_: Compute sum of input voxels.
|
|
621
|
+
abssum: Compute absolute sum of input voxels.
|
|
622
|
+
sos: Compute sum of squares.
|
|
623
|
+
l2norm: Compute L2 norm (sqrt(sum squares)).
|
|
624
|
+
mean: Compute mean of input voxels.
|
|
625
|
+
slope: Compute the slope of input voxels vs. time.
|
|
626
|
+
stdev: Compute standard deviation of input voxels.
|
|
627
|
+
stdev_nod: Compute standard deviation of input voxels without\
|
|
628
|
+
detrending.
|
|
629
|
+
cvar: Compute coefficient of variation of input voxels.
|
|
630
|
+
cvar_nod: Compute coefficient of variation of input voxels without\
|
|
631
|
+
detrending.
|
|
632
|
+
cvarinv: Compute inverse coefficient of variation of input voxels.
|
|
633
|
+
cvarinv_nod: Compute inverse coefficient of variation of input voxels\
|
|
634
|
+
without detrending.
|
|
635
|
+
tsnr: Compute temporal signal to noise ratio.
|
|
636
|
+
mad: Compute median absolute deviation of input voxels.
|
|
637
|
+
dw: Compute Durbin-Watson Statistic of input voxels.
|
|
638
|
+
median: Compute median of input voxels.
|
|
639
|
+
nzmedian: Compute median of non-zero input voxels.
|
|
640
|
+
nzstdev: Compute standard deviation of non-zero input voxels.
|
|
641
|
+
bmv: Compute biweight midvariance of input voxels.
|
|
642
|
+
mssd: Compute mean of successive squared differences of input voxels.
|
|
643
|
+
mssdsqrt: Compute square root of mean of successive squared differences\
|
|
644
|
+
of input voxels.
|
|
645
|
+
masdx: Compute median of absolute values of first time differences of\
|
|
646
|
+
input voxels.
|
|
647
|
+
min_: Compute minimum of input voxels.
|
|
648
|
+
max_: Compute maximum of input voxels.
|
|
649
|
+
absmax: Compute absolute maximum of input voxels.
|
|
650
|
+
signed_absmax: Compute signed absolute maximum of input voxels.
|
|
651
|
+
percentile: Compute the P-th percentile point of the data in each voxel\
|
|
652
|
+
time series.
|
|
653
|
+
argmin: Compute index of minimum of input voxels.
|
|
654
|
+
argmin1: Compute index + 1 of minimum of input voxels.
|
|
655
|
+
argmax: Compute index of maximum of input voxels.
|
|
656
|
+
argmax1: Compute index + 1 of maximum of input voxels.
|
|
657
|
+
argabsmax: Compute index of absolute maximum of input voxels.
|
|
658
|
+
argabsmax1: Compute index + 1 of absolute maximum of input voxels.
|
|
659
|
+
duration: Compute number of points around max above a threshold.
|
|
660
|
+
onset: Compute beginning of duration around max where value exceeds\
|
|
661
|
+
basepercent.
|
|
662
|
+
offset: Compute end of duration around max where value exceeds\
|
|
663
|
+
basepercent.
|
|
664
|
+
centroid: Compute centroid of data time curves.
|
|
665
|
+
centduration: Compute duration using centroid's index as center.
|
|
666
|
+
nzmean: Compute mean of non-zero voxels.
|
|
667
|
+
zcount: Count number of zero values at each voxel.
|
|
668
|
+
nzcount: Count number of non-zero values at each voxel.
|
|
669
|
+
autocorr: Compute autocorrelation function and return first n\
|
|
670
|
+
coefficients.
|
|
671
|
+
autoreg: Compute autoregression coefficients and return first n\
|
|
672
|
+
coefficients.
|
|
673
|
+
accumulate: Accumulate time series values (partial sums).
|
|
674
|
+
centromean: Compute mean of middle 50% of voxel values.
|
|
675
|
+
skewness: Measure of asymmetry in distribution.
|
|
676
|
+
kurtosis: Measure of the 'tailedness' of the probability distribution.
|
|
677
|
+
firstvalue: First value in dataset.
|
|
678
|
+
tdiff: Take the first difference of each time series before further\
|
|
679
|
+
processing.
|
|
680
|
+
prefix: Use string 'p' for the prefix of the output dataset [DEFAULT =\
|
|
681
|
+
'stat'].
|
|
682
|
+
datum: Use data type 'd' for the type of storage of the output, where\
|
|
683
|
+
'd' is one of 'byte', 'short', or 'float' [DEFAULT=float].
|
|
684
|
+
nscale: Do not scale output values when datum is byte or short. Scaling\
|
|
685
|
+
is done by default.
|
|
686
|
+
basepercent: Percentage of maximum for duration calculation.
|
|
687
|
+
mask_mset: Use the dataset 'mset' as a mask. Only voxels with nonzero\
|
|
688
|
+
values in 'mset' will be printed from 'dataset'.
|
|
689
|
+
mrange: Further restrict the voxels from 'mset' so that only those mask\
|
|
690
|
+
values between 'a' and 'b' (inclusive) will be used.
|
|
691
|
+
cmask: Execute the options enclosed in single quotes as a 3dcalc-like\
|
|
692
|
+
program, and produce a mask from the resulting 3D brick.
|
|
693
|
+
outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
|
|
694
|
+
runner: Command runner.
|
|
695
|
+
Returns:
|
|
696
|
+
NamedTuple of outputs (described in `V3dTstatOutputs`).
|
|
697
|
+
"""
|
|
698
|
+
runner = runner or get_global_runner()
|
|
699
|
+
execution = runner.start_execution(V_3D_TSTAT_METADATA)
|
|
700
|
+
params = v_3d_tstat_params(
|
|
701
|
+
mask=mask,
|
|
702
|
+
num_threads=num_threads,
|
|
703
|
+
sum_=sum_,
|
|
704
|
+
abssum=abssum,
|
|
705
|
+
sos=sos,
|
|
706
|
+
l2norm=l2norm,
|
|
707
|
+
mean=mean,
|
|
708
|
+
slope=slope,
|
|
709
|
+
stdev=stdev,
|
|
710
|
+
stdev_nod=stdev_nod,
|
|
711
|
+
cvar=cvar,
|
|
712
|
+
cvar_nod=cvar_nod,
|
|
713
|
+
cvarinv=cvarinv,
|
|
714
|
+
cvarinv_nod=cvarinv_nod,
|
|
715
|
+
tsnr=tsnr,
|
|
716
|
+
mad=mad,
|
|
717
|
+
dw=dw,
|
|
718
|
+
median=median,
|
|
719
|
+
nzmedian=nzmedian,
|
|
720
|
+
nzstdev=nzstdev,
|
|
721
|
+
bmv=bmv,
|
|
722
|
+
mssd=mssd,
|
|
723
|
+
mssdsqrt=mssdsqrt,
|
|
724
|
+
masdx=masdx,
|
|
725
|
+
min_=min_,
|
|
726
|
+
max_=max_,
|
|
727
|
+
absmax=absmax,
|
|
728
|
+
signed_absmax=signed_absmax,
|
|
729
|
+
percentile=percentile,
|
|
730
|
+
argmin=argmin,
|
|
731
|
+
argmin1=argmin1,
|
|
732
|
+
argmax=argmax,
|
|
733
|
+
argmax1=argmax1,
|
|
734
|
+
argabsmax=argabsmax,
|
|
735
|
+
argabsmax1=argabsmax1,
|
|
736
|
+
duration=duration,
|
|
737
|
+
onset=onset,
|
|
738
|
+
offset=offset,
|
|
739
|
+
centroid=centroid,
|
|
740
|
+
centduration=centduration,
|
|
741
|
+
nzmean=nzmean,
|
|
742
|
+
zcount=zcount,
|
|
743
|
+
nzcount=nzcount,
|
|
744
|
+
autocorr=autocorr,
|
|
745
|
+
autoreg=autoreg,
|
|
746
|
+
accumulate=accumulate,
|
|
747
|
+
centromean=centromean,
|
|
748
|
+
skewness=skewness,
|
|
749
|
+
kurtosis=kurtosis,
|
|
750
|
+
firstvalue=firstvalue,
|
|
751
|
+
tdiff=tdiff,
|
|
752
|
+
prefix=prefix,
|
|
753
|
+
datum=datum,
|
|
754
|
+
nscale=nscale,
|
|
755
|
+
basepercent=basepercent,
|
|
756
|
+
mask_mset=mask_mset,
|
|
757
|
+
mrange=mrange,
|
|
758
|
+
cmask=cmask,
|
|
759
|
+
outputtype=outputtype,
|
|
760
|
+
in_file=in_file,
|
|
761
|
+
)
|
|
762
|
+
return v_3d_tstat_execute(params, execution)
|
|
763
|
+
|
|
764
|
+
|
|
765
|
+
__all__ = [
|
|
766
|
+
"V3dTstatOutputs",
|
|
767
|
+
"V3dTstatParameters",
|
|
768
|
+
"V_3D_TSTAT_METADATA",
|
|
769
|
+
"v_3d_tstat",
|
|
770
|
+
"v_3d_tstat_params",
|
|
771
|
+
]
|