Merge pull request #1893 from FCP-INDI/bugfix/fs_ingress

Fix bugs in FreeSurfer tissue seg option

Author: sgiavasis

CPAC/pipeline/cpac_pipeline.py

@@ -1039,7 +1039,8 @@ def build_segmentation_stack(rpool, cfg, pipeline_blocks=None):
             not rpool.check_rpool('label-WM_mask'):
         seg_blocks = [
             [tissue_seg_fsl_fast,
-             tissue_seg_ants_prior]
+             tissue_seg_ants_prior,
+	     tissue_seg_freesurfer]
         ]
         if 'T1_Template' in cfg.segmentation['tissue_segmentation'][
             'Template_Based']['template_for_segmentation']:

CPAC/seg_preproc/seg_preproc.py

@@ -414,116 +414,6 @@ def create_seg_preproc_antsJointLabel_method(
     return preproc
 
 
-# def create_seg_preproc_freesurfer(config=None,
-#                                   wf_name='seg_preproc_freesurfer',
-#                                   pipe_num=0):
-#     """
-#     Generate the subject's segmentations based on freesurfer.
-
-#     Parameters
-#     ----------
-#     config : CPAC.utils.configuration.Configuration
-
-#     wf_name : string
-#         name of the workflow
-
-#     pipe_num : int
-
-#     Returns
-#     -------
-#     seg_preproc_freesurfer : workflow
-#         workflow object for segmentation workflow
-
-#     hemisphere_outputs : dict
-#         hemisphere-specific FreeSurfer outputs
-
-#     Notes
-#     -----
-
-#     Workflow Inputs: ::
-
-#         inputspec.subject_dir : string (existing nifti file)
-#             FreeSurfer autorecon1 dir
-
-#     Workflow Outputs: ::
-
-#         outputspec.wm_mask : string (nifti file)
-#             outputs White Matter mask
-#     """
-#     preproc = pe.Workflow(name=wf_name)
-
-#     inputnode = pe.Node(util.IdentityInterface(fields=['subject_dir']),
-#                         name='inputspec')
-
-#     outputnode = pe.Node(util.IdentityInterface(fields=['wm_mask',
-#                                                         'gm_mask',
-#                                                         'csf_mask',
-#                                                         'subject_id']),
-#                          name='outputspec')
-
-#     reconall2 = pe.Node(interface=freesurfer.ReconAll(),
-#                         name='anat_autorecon2')
-
-#     reconall2.inputs.directive = 'autorecon2'
-#     reconall2.inputs.openmp = config.pipeline_setup['system_config'][
-#         'num_omp_threads']
-
-#     preproc.connect(inputnode, 'subject_dir',
-#                     reconall2, 'subjects_dir')
-
-#     preproc.connect(reconall2, 'subject_id',
-#                     outputnode, 'subject_id')
-
-#     # register FS segmentations (aseg.mgz) to native space
-#     fs_aseg_to_native = pe.Node(interface=freesurfer.ApplyVolTransform(),
-#                                 name='fs_aseg_to_native')
-
-#     fs_aseg_to_native.inputs.reg_header = True
-#     fs_aseg_to_native.inputs.interp = 'nearest'
-
-#     preproc.connect(reconall2, 'aseg',
-#                     fs_aseg_to_native, 'source_file')
-
-#     preproc.connect(reconall2, 'rawavg',
-#                     fs_aseg_to_native, 'target_file')
-
-#     preproc.connect(inputnode, 'subject_dir',
-#                     fs_aseg_to_native, 'subjects_dir')
-
-#     # convert registered FS segmentations from .mgz to .nii.gz
-#     fs_aseg_to_nifti = pe.Node(util.Function(input_names=['in_file'],
-#                                              output_names=['out_file'],
-#                                              function=mri_convert),
-#                                name='fs_aseg_to_nifti')
-
-#     fs_aseg_to_nifti.inputs.args = '-rt nearest'
-
-#     preproc.connect(fs_aseg_to_native, 'transformed_file',
-#                     fs_aseg_to_nifti, 'in_file')
-
-#     pick_tissue = pe.Node(
-#         pick_tissue_from_labels_file_interface(
-#             input_names=['multiatlas_Labels']),
-#         name=f'{wf_name}_tissue_mask')
-
-#     preproc.connect(fs_aseg_to_nifti, 'out_file',
-#                     pick_tissue, 'multiatlas_Labels')
-
-#     preproc.connect(pick_tissue, 'wm_mask',
-#                     outputnode, 'wm_mask')
-
-#     preproc.connect(pick_tissue, 'gm_mask',
-#                     outputnode, 'gm_mask')
-
-#     preproc.connect(pick_tissue, 'csf_mask',
-#                     outputnode, 'csf_mask')
-
-#     preproc, hemisphere_outputs = freesurfer_hemispheres(preproc, reconall2,
-#                                                          pipe_num)
-
-#     return preproc, hemisphere_outputs
-
-
 def tissue_seg_fsl_fast(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
     {"name": "tissue_seg_fsl_fast",
@@ -934,9 +824,6 @@ def tissue_seg_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
                                name=f'fs_aseg_to_nifti_{pipe_num}')
     fs_aseg_to_nifti.inputs.args = '-rt nearest'
 
-    wf.connect(fs_aseg_to_native, 'transformed_file',
-               fs_aseg_to_nifti, 'in_file')
-
     pick_tissue = pe.Node(pick_tissue_from_labels_file_interface(),
                           name=f'select_fs_tissue_{pipe_num}')
 
@@ -962,27 +849,17 @@ def tissue_seg_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
                        'in_file')
 
     if erode_tissues:
-        outputs['label-CSF_mask'] = (erode_tissues['csf'], 'binary_file')
-        outputs['label-WM_mask'] = (erode_tissues['wm'], 'binary_file')
-        outputs['label-GM_mask'] = (erode_tissues['gm'], 'binary_file')
+        outputs = {
+            'label-CSF_mask': (erode_tissues['csf'], 'binary_file'), 
+            'label-WM_mask': (erode_tissues['wm'], 'binary_file'),
+            'label-GM_mask': (erode_tissues['gm'], 'binary_file')
+            }
 
     else:
-        outputs['label-CSF_mask'] = (pick_tissue, 'csf_mask')
-        outputs['label-WM_mask'] = (pick_tissue, 'wm_mask')
-        outputs['label-GM_mask'] = (pick_tissue, 'gm_mask')
-
-    fs_seg, hemisphere_outputs = create_seg_preproc_freesurfer(
-        config=cfg, wf_name=f'seg_preproc_freesurfer_{pipe_num}',
-        pipe_num=pipe_num)
-
-    node, out = strat_pool.get_data('freesurfer-subject-dir')
-    wf.connect(node, out, fs_seg, 'inputspec.subject_dir')
-
-    outputs = {
-        'label-CSF_mask': (fs_seg, 'outputspec.csf_mask'),
-        'label-GM_mask': (fs_seg, 'outputspec.gm_mask'),
-        'label-WM_mask': (fs_seg, 'outputspec.wm_mask'),
-        **hemisphere_outputs
-    }
+        outputs = {
+            'label-CSF_mask': (pick_tissue, 'csf_mask'),
+            'label-WM_mask': (pick_tissue, 'wm_mask'),
+            'label-GM_mask': (pick_tissue, 'gm_mask')
+        }
 
     return (wf, outputs)