diff --git a/skullTo3d/pipelines/rename.py b/skullTo3d/pipelines/rename.py index 3f39274..24f8608 100644 --- a/skullTo3d/pipelines/rename.py +++ b/skullTo3d/pipelines/rename.py @@ -46,6 +46,22 @@ def rename_all_skull_petra_derivatives(params, main_workflow, segment_pnh_pipe, rename_stereo_petra_skull_mask, 'out_file', datasink, '@stereo_petra_skull_mask') + # rename petra_head_stl + rename_petra_head_stl = pe.Node(niu.Rename(), + name="rename_petra_head_stl") + rename_petra_head_stl.inputs.format_string = \ + pref_deriv + "_desc-petra_headmask" + rename_petra_head_stl.inputs.parse_string = parse_str + rename_petra_head_stl.inputs.keep_ext = True + + main_workflow.connect( + skull_petra_pipe, 'outputnode.petra_head_stl', + rename_petra_head_stl, 'in_file') + + main_workflow.connect( + rename_petra_head_stl, 'out_file', + datasink, '@petra_head_stl') + # rename stereo_petra_head_mask rename_stereo_petra_head_mask = pe.Node( niu.Rename(), name="rename_stereo_petra_head_mask") diff --git a/skullTo3d/pipelines/skull_pipe.py b/skullTo3d/pipelines/skull_pipe.py index 2e04fca..4dbde06 100644 --- a/skullTo3d/pipelines/skull_pipe.py +++ b/skullTo3d/pipelines/skull_pipe.py @@ -805,6 +805,14 @@ def create_autonomous_skull_petra_pipe(name="skull_petra_pipe", params={}): inputnode, ('indiv_params', parse_key, "petra_head_erode"), petra_head_erode, "indiv_params") + # mesh_petra_head ####### + mesh_petra_head = pe.Node( + interface=IsoSurface(), + name="mesh_petra_head") + + skull_petra_pipe.connect(petra_head_erode, "out_file", + mesh_petra_head, "nii_file") + # ### Masking with head mask # petra_hmasked ####### [okey] petra_hmasked = pe.Node(interface=ApplyMask(), @@ -1033,7 +1041,7 @@ def create_autonomous_skull_petra_pipe(name="skull_petra_pipe", params={}): niu.IdentityInterface( fields=["petra_skull_mask", "petra_skull_stl", "robustpetra_skull_mask", "robustpetra_skull_stl", - "petra_head_mask"]), + "petra_head_mask", "petra_head_stl"]), name='outputnode') skull_petra_pipe.connect(petra_head_erode, "out_file", @@ -1042,6 +1050,9 @@ def create_autonomous_skull_petra_pipe(name="skull_petra_pipe", params={}): skull_petra_pipe.connect(mesh_petra_skull, "stl_file", outputnode, "petra_skull_stl") + skull_petra_pipe.connect(mesh_petra_head, "stl_file", + outputnode, "petra_head_stl") + skull_petra_pipe.connect(petra_skull_erode, "out_file", outputnode, "petra_skull_mask") @@ -1260,6 +1271,14 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}): inputnode, ('indiv_params', parse_key, "petra_head_erode"), petra_head_erode, "indiv_params") + # mesh_petra_head ####### + mesh_petra_head = pe.Node( + interface=IsoSurface(), + name="mesh_petra_head") + + skull_petra_pipe.connect(petra_head_erode, "out_file", + mesh_petra_head, "nii_file") + # ### Masking with head mask # petra_hmasked ####### [okey] petra_hmasked = pe.Node(interface=ApplyMask(), @@ -1483,12 +1502,15 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}): niu.IdentityInterface( fields=["petra_skull_mask", "petra_skull_stl", "robustpetra_skull_mask", "robustpetra_skull_stl", - "petra_head_mask"]), + "petra_head_mask", "petra_head_stl"]), name='outputnode') skull_petra_pipe.connect(petra_head_erode, "out_file", outputnode, "petra_head_mask") + skull_petra_pipe.connect(mesh_petra_head, "stl_file", + outputnode, "petra_head_stl") + skull_petra_pipe.connect(mesh_petra_skull, "stl_file", outputnode, "petra_skull_stl") diff --git a/workflows/params_segment_marmo_ants_skull.json b/workflows/params_segment_marmo_ants_skull.json index 9a379a8..98851da 100755 --- a/workflows/params_segment_marmo_ants_skull.json +++ b/workflows/params_segment_marmo_ants_skull.json @@ -29,10 +29,6 @@ "ln_val": 17, "lp_val": 15, "smoo_r_val": 1.0 - }, - "crop_z_T1": - { - "brainsize": 30 } }, "pad_template":