Cleanup

Author: jpellman

docs/user/_sources/_static/outputs.csv

@@ -1,151 +1,132 @@
-strat.update_resource_pool({'anatomical_brain':(anat_preproc,'outputspec.brain')})
-strat.update_resource_pool({'anatomical_reorient':(anat_preproc,'outputspec.reorient')})
-strat.update_resource_pool({'anatomical_to_mni_linear_xfm':(fnirt_reg_anat_mni,'outputspec.linear_xfm'),
-'anatomical_to_mni_nonlinear_xfm':(fnirt_reg_anat_mni,'outputspec.nonlinear_xfm'),
-'mni_to_anatomical_linear_xfm':(fnirt_reg_anat_mni,'outputspec.invlinear_xfm'),
-'mni_normalized_anatomical':(fnirt_reg_anat_mni,'outputspec.output_brain')})
-strat.update_resource_pool({'ants_initial_xfm':(ants_reg_anat_mni,'outputspec.ants_initial_xfm'),
-'ants_rigid_xfm':(ants_reg_anat_mni,'outputspec.ants_rigid_xfm'),
-'ants_affine_xfm':(ants_reg_anat_mni,'outputspec.ants_affine_xfm'),
-'anatomical_to_mni_nonlinear_xfm':(ants_reg_anat_mni,'outputspec.warp_field'),
-'mni_to_anatomical_nonlinear_xfm':(ants_reg_anat_mni,'outputspec.inverse_warp_field'),
-'anat_to_mni_ants_composite_xfm':(ants_reg_anat_mni,'outputspec.composite_transform'),
-'mni_normalized_anatomical':(ants_reg_anat_mni,'outputspec.normalized_output_brain')})
-strat.update_resource_pool({'anatomical_to_symmetric_mni_linear_xfm':(fnirt_reg_anat_symm_mni,'outputspec.linear_xfm'),
-'anatomical_to_symmetric_mni_nonlinear_xfm':(fnirt_reg_anat_symm_mni,'outputspec.nonlinear_xfm'),
-'symmetric_mni_to_anatomical_linear_xfm':(fnirt_reg_anat_symm_mni,'outputspec.invlinear_xfm'),
-'symmetric_mni_normalized_anatomical':(fnirt_reg_anat_symm_mni,'outputspec.output_brain')})#,
-#'mni_normalized_anatomical':(ants_reg_anat_symm_mni,'outputspec.wait')})
-strat.update_resource_pool({'ants_symmetric_initial_xfm':(ants_reg_anat_symm_mni,'outputspec.ants_initial_xfm'),
-'ants_symmetric_rigid_xfm':(ants_reg_anat_symm_mni,'outputspec.ants_rigid_xfm'),
-'ants_symmetric_affine_xfm':(ants_reg_anat_symm_mni,'outputspec.ants_affine_xfm'),
-'anatomical_to_symmetric_mni_nonlinear_xfm':(ants_reg_anat_symm_mni,'outputspec.warp_field'),
-'symmetric_mni_to_anatomical_nonlinear_xfm':(ants_reg_anat_symm_mni,'outputspec.inverse_warp_field'),
-'anat_to_symmetric_mni_ants_composite_xfm':(ants_reg_anat_symm_mni,'outputspec.composite_transform'),
-'symmetric_mni_normalized_anatomical':(ants_reg_anat_symm_mni,'outputspec.normalized_output_brain')})#,
-#'mni_normalized_anatomical':(ants_reg_anat_symm_mni,'outputspec.wait')})
-strat.update_resource_pool({'anatomical_gm_mask':(seg_preproc,'outputspec.gm_mask'),
-'anatomical_csf_mask':(seg_preproc,'outputspec.csf_mask'),
-'anatomical_wm_mask':(seg_preproc,'outputspec.wm_mask'),
-'seg_probability_maps':(seg_preproc,'outputspec.probability_maps'),
-'seg_mixeltype':(seg_preproc,'outputspec.mixeltype'),
-'seg_partial_volume_map':(seg_preproc,'outputspec.partial_volume_map'),
-'seg_partial_volume_files':(seg_preproc,'outputspec.partial_volume_files')})
-strat.update_resource_pool({'raw_functional':(funcFlow,'outputspec.rest')})
-strat.update_resource_pool({'selected_func_volume':(get_func_volume,'out_file')})
-strat.update_resource_pool({'slice_time_corrected':(func_slice_timing_correction,'out_file')})
-strat.update_resource_pool({'mean_functional':(func_preproc,'outputspec.example_func')})
-strat.update_resource_pool({'functional_preprocessed_mask':(func_preproc,'outputspec.preprocessed_mask')})
-strat.update_resource_pool({'movement_parameters':(func_preproc,'outputspec.movement_parameters')})
-strat.update_resource_pool({'max_displacement':(func_preproc,'outputspec.max_displacement')})
-strat.update_resource_pool({'preprocessed':(func_preproc,'outputspec.preprocessed')})
-strat.update_resource_pool({'functional_brain_mask':(func_preproc,'outputspec.mask')})
-strat.update_resource_pool({'motion_correct':(func_preproc,'outputspec.motion_correct')})
-strat.update_resource_pool({'coordinate_transformation':(func_preproc,'outputspec.oned_matrix_save')})
-strat.update_resource_pool({'mean_functional':(func_preproc,'outputspec.example_func')})
-strat.update_resource_pool({'functional_preprocessed_mask':(func_preproc,'outputspec.preprocessed_mask')})
-strat.update_resource_pool({'movement_parameters':(func_preproc,'outputspec.movement_parameters')})
-strat.update_resource_pool({'max_displacement':(func_preproc,'outputspec.max_displacement')})
-strat.update_resource_pool({'preprocessed':(func_preproc,'outputspec.preprocessed')})
-strat.update_resource_pool({'functional_brain_mask':(func_preproc,'outputspec.mask')})
-strat.update_resource_pool({'motion_correct':(func_preproc,'outputspec.motion_correct')})
-strat.update_resource_pool({'coordinate_transformation':(func_preproc,'outputspec.oned_matrix_save')})
-strat.update_resource_pool({'movement_parameters':(fristons_model,'outputspec.movement_file')})
-strat.update_resource_pool({'mean_functional_in_anat':(func_to_anat,'outputspec.anat_func_nobbreg'),
-'functional_to_anat_linear_xfm':(func_to_anat,'outputspec.func_to_anat_linear_xfm_nobbreg')})
-strat.update_resource_pool({'mean_functional_in_anat':(func_to_anat_bbreg,'outputspec.anat_func'),
-'functional_to_anat_linear_xfm':(func_to_anat_bbreg,'outputspec.func_to_anat_linear_xfm')})
-strat.update_resource_pool({'frame_wise_displacement':(gen_motion_stats,'outputspec.FD_1D'),
-'scrubbing_frames_excluded':(gen_motion_stats,'outputspec.frames_ex_1D'),
-'scrubbing_frames_included':(gen_motion_stats,'outputspec.frames_in_1D'),
-'power_params':(gen_motion_stats,'outputspec.power_params'),
-'motion_params':(gen_motion_stats,'outputspec.motion_params')})
-strat.update_resource_pool({'functional_nuisance_residuals':(nuisance,'outputspec.subject')})
-strat.update_resource_pool({'functional_median_angle_corrected':(median_angle_corr,'outputspec.subject')})
-strat.update_resource_pool({'alff_img':(alff,'outputspec.alff_img')})
-strat.update_resource_pool({'falff_img':(alff,'outputspec.falff_img')})
-strat.update_resource_pool({'functional_freq_filtered':(frequency_filter,'bandpassed_file')})
-strat.update_resource_pool({'scrubbing_movement_parameters':(scrubbing,'outputspec.scrubbed_movement_parameters'),
-'scrubbed_preprocessed':(scrubbing,'outputspec.preprocessed')})
-strat.update_resource_pool({'functional_mni':(func_mni_warp,'out_file'),
-'functional_brain_mask_to_standard':(functional_brain_mask_to_standard,'out_file'),
-'mean_functional_in_mni':(mean_functional_warp,'out_file'),
-'motion_correct_to_standard':(motion_correct_warp,'out_file')})
-strat.update_resource_pool({'itk_func_anat_affine_%s'%\
-(func_name):(fsl_to_itk_func_mni,\
-'outputspec.itk_transform')})
-strat.update_resource_pool({'itk_collected_warps_%s'%\
-(func_name):(collect_transforms_func_mni,\
-'outputspec.transformation_series')})
-strat.update_resource_pool({func_name:\
-(apply_ants_warp_func_mni,\
-'outputspec.output_image')})
-strat.update_resource_pool({'vmhc_raw_score':(vmhc,'outputspec.VMHC_FWHM_img')})
-strat.update_resource_pool({'vmhc_fisher_zstd':(vmhc,'outputspec.VMHC_Z_FWHM_img')})
-strat.update_resource_pool({'vmhc_fisher_zstd_zstat_map':(vmhc,'outputspec.VMHC_Z_stat_FWHM_img')})
-strat.update_resource_pool({'raw_reho_map':(reho,'outputspec.raw_reho_map')})
-strat.update_resource_pool({'spatial_map_timeseries':(spatial_map_timeseries,'outputspec.subject_timeseries')})
-strat.update_resource_pool({'roi_timeseries':(roi_timeseries,'outputspec.roi_outputs')})
-strat.update_resource_pool({'roi_timeseries_for_SCA':(roi_timeseries_for_sca,'outputspec.roi_outputs')})
-strat.update_resource_pool({'voxel_timeseries':(voxel_timeseries,'outputspec.mask_outputs')})
-strat.update_resource_pool({'voxel_timeseries_for_SCA':(voxel_timeseries_for_sca,'outputspec.mask_outputs')})
-strat.update_resource_pool({'sca_roi_correlation_stack':(sca_roi,'outputspec.correlation_stack'),
-'sca_roi_correlation_files':(sca_roi,'outputspec.correlation_files')})
-strat.update_resource_pool({'sca_seed_correlation_files':(sca_seed,'outputspec.correlation_files')})
-strat.update_resource_pool({'dr_tempreg_maps_stack':(dr_temp_reg,'outputspec.temp_reg_map'),
-'dr_tempreg_maps_files':(dr_temp_reg,'outputspec.temp_reg_map_files')})
-strat.update_resource_pool({'dr_tempreg_maps_zstat_stack':(dr_temp_reg,'outputspec.temp_reg_map_z'),
-'dr_tempreg_maps_zstat_files':(dr_temp_reg,'outputspec.temp_reg_map_z_files')})
-strat.update_resource_pool({'sca_tempreg_maps_stack':(sc_temp_reg,'outputspec.temp_reg_map'),
-'sca_tempreg_maps_files':(sc_temp_reg,'outputspec.temp_reg_map_files')})
-strat.update_resource_pool({'sca_tempreg_maps_zstat_stack':(sc_temp_reg,'outputspec.temp_reg_map_z'),
-'sca_tempreg_maps_zstat_files':(sc_temp_reg,'outputspec.temp_reg_map_z_files')})
-strat.update_resource_pool({'bbregister_registration':(surface_reg,'outputspec.out_reg_file'),
-'left_hemisphere_surface':(surface_reg,'outputspec.lh_surface_file'),
-'right_hemisphere_surface':(surface_reg,'outputspec.rh_surface_file')})
-strat.update_resource_pool({'vertices_timeseries':(vertices_timeseries,'outputspec.surface_outputs')})
-strat.update_resource_pool({'centrality_outputs':(merge_node,'merged_list')})
-strat.update_resource_pool({'centrality_outputs_zstd':(z_score,'outputspec.z_score_img'),
-'centrality_outputs_smoothed':(smoothing,'out_file'),
-'centrality_outputs_smoothed_zstd':(zstd_smoothing,'out_file')})
-strat.update_resource_pool({'%s_to_standard'%(output_name):\
-(apply_ants_warp,'outputspec.output_image')})
-strat.update_resource_pool({'%s_to_standard'%(output_name):\
-(apply_fsl_warp,'out_file')})
-strat.update_resource_pool({'%s_smooth'%(output_name):\
-(output_smooth,'out_file')})
-strat.update_resource_pool({'%s_to_standard_smooth'%\
-(output_name):(output_to_standard_smooth,'out_file')})
-strat.update_resource_pool({'%s_zstd'%(output_resource):\
-(z_score_std,'outputspec.z_score_img')})
-strat.update_resource_pool({'%s_fisher_zstd'%(output_resource):\
-(fisher_z_score_std,'outputspec.fisher_z_score_img')})
-strat.update_resource_pool({'output_means.@%s_average'%(output_resource):(mean_to_csv,'output_mean')})
-strat.update_resource_pool({'sca_tempreg_maps_stack_smooth':(sc_temp_reg_maps_smooth,'out_file'),
-'sca_tempreg_maps_files_smooth':(sc_temp_reg_maps_files_smooth,'out_file'),
-'sca_tempreg_maps_zstat_stack_smooth':(sc_temp_reg_maps_Z_stack_smooth,'out_file'),
-'sca_tempreg_maps_zstat_files_smooth':(sc_temp_reg_maps_Z_files_smooth,'out_file')})
-strat.update_resource_pool({'dr_tempreg_maps_stack_to_standard_smooth':(dr_temp_reg_maps_smooth,'out_file'),
-'dr_tempreg_maps_zstat_stack_to_standard_smooth':(dr_temp_reg_maps_Z_stack_smooth,'out_file'),
-'dr_tempreg_maps_files_to_standard_smooth':(dr_temp_reg_maps_files_smooth,'out_file'),
-'dr_tempreg_maps_zstat_files_to_standard_smooth':(dr_temp_reg_maps_Z_files_smooth,'out_file')})
-strat.update_resource_pool({'qc___snr_a':(montage_snr,'outputspec.axial_png'),
-'qc___snr_s':(montage_snr,'outputspec.sagittal_png'),
-'qc___snr_hist':(hist_,'hist_path'),
-'qc___snr_val':(snr_val,'snr_storefl')})###
-strat.update_resource_pool({'qc___movement_trans_plot':(mov_plot,'translation_plot'),
-'qc___movement_rot_plot':(mov_plot,'rotation_plot')})
-strat.update_resource_pool({'qc___fd_plot':(fd_plot,'hist_path')})
-strat.update_resource_pool({'qc___skullstrip_vis_a':(montage_skull,'outputspec.axial_png'),
-'qc___skullstrip_vis_s':(montage_skull,'outputspec.sagittal_png')})
-strat.update_resource_pool({'qc___mni_normalized_anatomical_a':(montage_mni_anat,'outputspec.axial_png'),
-'qc___mni_normalized_anatomical_s':(montage_mni_anat,'outputspec.sagittal_png')})
-strat.update_resource_pool({'qc___csf_gm_wm_a':(montage_csf_gm_wm,'outputspec.axial_png'),
-'qc___csf_gm_wm_s':(montage_csf_gm_wm,'outputspec.sagittal_png')})
-strat.update_resource_pool({'qc___mean_func_with_t1_edge_a':(montage_anat,'outputspec.axial_png'),
-'qc___mean_func_with_t1_edge_s':(montage_anat,'outputspec.sagittal_png')})
-strat.update_resource_pool({'qc___mean_func_with_mni_edge_a':(montage_mfi,'outputspec.axial_png'),
-'qc___mean_func_with_mni_edge_s':(montage_mfi,'outputspec.sagittal_png')})
-strat.update_resource_pool({'qc___%s_a'%measure:(montage,'outputspec.axial_png'),
-'qc___%s_s'%measure:(montage,'outputspec.sagittal_png'),
-'qc___%s_hist'%measure:(histogram,'hist_path')})
+alff_img
+anatomical_brain
+anatomical_csf_mask
+anatomical_gm_mask
+anatomical_reorient
+anatomical_to_mni_linear_xfm
+anatomical_to_mni_nonlinear_xfm
+anatomical_to_symmetric_mni_linear_xfm
+anatomical_to_symmetric_mni_nonlinear_xfm
+anatomical_wm_mask
+anat_to_mni_ants_composite_xfm
+anat_to_symmetric_mni_ants_composite_xfm
+ants_affine_xfm
+ants_initial_xfm
+ants_rigid_xfm
+ants_symmetric_affine_xfm
+ants_symmetric_initial_xfm
+ants_symmetric_rigid_xfm
+apply_ants_warp_func_mni
+apply_ants_warpoutputspec.output_image
+apply_fsl_warpout_file
+bbregister_registration
+centrality_outputs
+centrality_outputs_smoothed
+centrality_outputs_smoothed_zstd
+centrality_outputs_zstd
+coordinate_transformation
+dr_tempreg_maps_files
+dr_tempreg_maps_files_to_standard_smooth
+dr_tempreg_maps_stack
+dr_tempreg_maps_stack_to_standard_smooth
+dr_tempreg_maps_zstat_files
+dr_tempreg_maps_zstat_files_to_standard_smooth
+dr_tempreg_maps_zstat_stack
+dr_tempreg_maps_zstat_stack_to_standard_smooth
+falff_img
+fisher_z_score_stdoutputspec.fisher_z_score_img
+frame_wise_displacement
+func_name
+functional_brain_mask
+functional_brain_mask_to_standard
+functional_freq_filtered
+functional_median_angle_corrected
+functional_mni
+functional_nuisance_residuals
+functional_preprocessed_mask
+functional_to_anat_linear_xfm
+itk_collected_warps_%s
+itk_func_anat_affine_%s
+left_hemisphere_surface
+max_displacement
+mean_functional
+mean_functional_in_anat
+mean_functional_in_mni
+#mni_normalized_anatomical
+mni_normalized_anatomical
+mni_to_anatomical_linear_xfm
+mni_to_anatomical_nonlinear_xfm
+motion_correct
+motion_correct_to_standard
+motion_params
+movement_parameters
+output_means.@%s_average%output_resource
+output_name
+output_smoothout_file
+outputspec.itk_transform
+outputspec.output_image
+outputspec.transformation_series
+power_params
+preprocessed
+qc___csf_gm_wm_a
+qc___csf_gm_wm_s
+qc___fd_plot
+qc___mean_func_with_mni_edge_a
+qc___mean_func_with_mni_edge_s
+qc___mean_func_with_t1_edge_a
+qc___mean_func_with_t1_edge_s
+qc___mni_normalized_anatomical_a
+qc___mni_normalized_anatomical_s
+qc___movement_rot_plot
+qc___movement_trans_plot
+qc___%s_a%measure
+qc___%s_hist%measure
+qc___skullstrip_vis_a
+qc___skullstrip_vis_s
+qc___snr_a
+qc___snr_hist
+qc___snr_s
+qc___snr_val
+qc___%s_s%measure
+raw_functional
+raw_reho_map
+right_hemisphere_surface
+roi_timeseries
+roi_timeseries_for_SCA
+sca_roi_correlation_files
+sca_roi_correlation_stack
+sca_seed_correlation_files
+sca_tempreg_maps_files
+sca_tempreg_maps_files_smooth
+sca_tempreg_maps_stack
+sca_tempreg_maps_stack_smooth
+sca_tempreg_maps_zstat_files
+sca_tempreg_maps_zstat_files_smooth
+sca_tempreg_maps_zstat_stack
+sca_tempreg_maps_zstat_stack_smooth
+scrubbed_preprocessed
+scrubbing_frames_excluded
+scrubbing_frames_included
+scrubbing_movement_parameters
+seg_mixeltype
+seg_partial_volume_files
+seg_partial_volume_map
+seg_probability_maps
+selected_func_volume
+%s_fisher_zstd%output_resource
+slice_time_corrected
+spatial_map_timeseries
+%s_smooth%output_name
+%s_to_standard%output_name
+%s_to_standard_smooth%\
+symmetric_mni_normalized_anatomical
+symmetric_mni_to_anatomical_linear_xfm
+symmetric_mni_to_anatomical_nonlinear_xfm
+%s_zstd%output_resource
+vertices_timeseries
+vmhc_fisher_zstd
+vmhc_fisher_zstd_zstat_map
+vmhc_raw_score
+voxel_timeseries
+voxel_timeseries_for_SCA
+z_score_stdoutputspec.z_score_img