fix the merge error about skullstrip_option in cpac_pipeline.py

Author: HechengJin0

CPAC/pipeline/cpac_pipeline.py

@@ -1087,27 +1087,6 @@ def build_workflow(subject_id, sub_dict, c, pipeline_name=None, num_ants_cores=1
 
                     new_strat_list += [new_strat]
 
-                    if "FSL" in c.skullstrip_option:
-                        anat_preproc = create_anat_preproc(method='fsl',
-                                                        config=c,
-                                                        wf_name='anat_preproc_bet_%d' % num_strat)
-
-                        anat_preproc.inputs.BET_options.set(
-                            frac=c.bet_frac,
-                            mask_boolean=c.bet_mask_boolean,
-                            mesh_boolean=c.bet_mesh_boolean,
-                            outline=c.bet_outline,
-                            padding=c.bet_padding,
-                            radius=c.bet_radius,
-                            reduce_bias=c.bet_reduce_bias,
-                            remove_eyes=c.bet_remove_eyes,
-                            robust=c.bet_robust,
-                            skull=c.bet_skull,
-                            surfaces=c.bet_surfaces,
-                            threshold=c.bet_threshold,
-                            vertical_gradient=c.bet_vertical_gradient,
-                        )
-
                 if "unet" in c.skullstrip_option:
                     anat_preproc = create_anat_preproc(method='unet',
                                                     config=c,
@@ -1130,87 +1109,6 @@ def build_workflow(subject_id, sub_dict, c, pipeline_name=None, num_ants_cores=1
                         'anatomical_brain_mask': (anat_preproc, 'outputspec.brain_mask'),
                     })
 
-                    if "niworkflows-ants" in c.skullstrip_option:
-                        anat_preproc = create_anat_preproc(method='niworkflows-ants',
-                                                        config=c,
-                                                        wf_name='anat_preproc_niworkflows_ants_%d' % num_strat)
-
-                    new_strat = strat.fork()
-                    node, out_file = new_strat['anatomical']
-                    workflow.connect(node, out_file,
-                                    anat_preproc, 'inputspec.anat')
-                    new_strat.append_name(anat_preproc.name)
-                    new_strat.set_leaf_properties(anat_preproc, 'outputspec.brain')
-                    new_strat.update_resource_pool({
-                        'anatomical_brain': (anat_preproc, 'outputspec.brain'),
-                        'anatomical_skull_leaf': (anat_preproc, 'outputspec.anat_skull_leaf'),
-                        'anatomical_brain_mask': (anat_preproc, 'outputspec.brain_mask'),
-                    })
-
-                    new_strat_list += [new_strat]
-
-                if "unet" in c.skullstrip_option:
-                    anat_preproc = create_anat_preproc(method='unet',
-                                                    config=c,
-                                                    acpc_target=acpc_target,
-                                                    wf_name='anat_preproc_unet_%d' % num_strat)
-
-                    new_strat = strat.fork()
-                    node, out_file = new_strat['anatomical']
-                    workflow.connect(node, out_file,
-                                    anat_preproc, 'inputspec.anat')
-                    workflow.connect(c.acpc_template_skull, 'local_path',
-                                    anat_preproc, 'inputspec.template_skull_for_anat')                               
-                    workflow.connect(c.acpc_template_brain, 'local_path',
-                                    anat_preproc, 'inputspec.template_brain_only_for_anat')
-                    new_strat.append_name(anat_preproc.name)
-                    new_strat.set_leaf_properties(anat_preproc, 'outputspec.brain')
-                    new_strat.update_resource_pool({
-                        'anatomical_brain': (anat_preproc, 'outputspec.brain'),
-                        'anatomical_skull_leaf': (anat_preproc, 'outputspec.anat_skull_leaf'),
-                        'anatomical_brain_mask': (anat_preproc, 'outputspec.brain_mask'),
-                    })
-
-                    if "niworkflows-ants" in c.skullstrip_option:
-                        anat_preproc = create_anat_preproc(method='niworkflows-ants',
-                                                        config=c,
-                                                        wf_name='anat_preproc_niworkflows_ants_%d' % num_strat)
-
-                        new_strat = strat.fork()
-                        node, out_file = new_strat['anatomical']
-                        workflow.connect(node, out_file,
-                                        anat_preproc, 'inputspec.anat')
-                        new_strat.append_name(anat_preproc.name)
-                        new_strat.set_leaf_properties(anat_preproc, 'outputspec.brain')
-                        new_strat.update_resource_pool({
-                            'anatomical_brain': (anat_preproc, 'outputspec.brain'),
-                            'anatomical_reorient': (anat_preproc, 'outputspec.reorient'),
-                            'anatomical_brain_mask': (anat_preproc, 'outputspec.brain_mask'),
-                        })
-
-                    new_strat_list += [new_strat]
-
-                if "unet" in c.skullstrip_option:
-                    anat_preproc = create_anat_preproc(method='unet',
-                                                    config=c,
-                                                    wf_name='anat_preproc_unet_%d' % num_strat)
-
-                    new_strat = strat.fork()
-                    node, out_file = new_strat['anatomical']
-                    workflow.connect(node, out_file,
-                                    anat_preproc, 'inputspec.anat')
-                    workflow.connect(c.acpc_template_skull, 'local_path',
-                                    anat_preproc, 'inputspec.template_skull_for_anat')                               
-                    workflow.connect(c.acpc_template_brain, 'local_path',
-                                    anat_preproc, 'inputspec.template_brain_only_for_anat')
-                    new_strat.append_name(anat_preproc.name)
-                    new_strat.set_leaf_properties(anat_preproc, 'outputspec.brain')
-                    new_strat.update_resource_pool({
-                        'anatomical_brain': (anat_preproc, 'outputspec.brain'),
-                        'anatomical_skull_leaf': (anat_preproc, 'outputspec.anat_skull_leaf'),
-                        'anatomical_brain_mask': (anat_preproc, 'outputspec.brain_mask'),
-                    })
-
                     new_strat_list += [new_strat]