[ENH] stl by seg tissue (#308)

* IsoSurface_tissues_pipe

Author: davidmeunier79

macapype/pipelines/full_pipelines.py

@@ -34,7 +34,8 @@
 
 from .extract_brain import create_extract_pipe
 
-from .surface import (create_nii2mesh_brain_pipe, create_IsoSurface_brain_pipe)
+from .surface import (create_nii2mesh_brain_pipe, create_IsoSurface_brain_pipe,
+                      create_IsoSurface_tissues_pipe)
 
 from macapype.utils.misc import parse_key, list_input_files
 
@@ -965,6 +966,10 @@ def create_full_ants_subpipes(
                     "native_wmgm_mask",
                     "wmgm_stl",
 
+                    "csf_stl",
+                    "gm_stl",
+                    "wm_stl",
+
                     "stereo_to_native_trans",
                     "native_to_stereo_trans"]),
         name='outputnode')
@@ -1513,6 +1518,30 @@ def create_full_ants_subpipes(
                 IsoSurface_brain_pipe, "outputnode.wmgm_nii",
                 outputnode, "native_wmgm_mask", params)
 
+    if "IsoSurface_tissues_pipe" in params["brain_segment_pipe"]:
+
+        IsoSurface_tissues_pipe = create_IsoSurface_tissues_pipe(
+            params=parse_key(params["brain_segment_pipe"],
+                             "IsoSurface_tissues_pipe"))
+
+        seg_pipe.connect(brain_segment_pipe, "outputnode.threshold_csf",
+                         IsoSurface_tissues_pipe, 'inputnode.threshold_csf')
+
+        seg_pipe.connect(brain_segment_pipe, "outputnode.threshold_wm",
+                         IsoSurface_tissues_pipe, 'inputnode.threshold_wm')
+
+        seg_pipe.connect(brain_segment_pipe, "outputnode.threshold_gm",
+                         IsoSurface_tissues_pipe, 'inputnode.threshold_gm')
+
+        seg_pipe.connect(IsoSurface_tissues_pipe, "outputnode.csf_stl",
+                         outputnode, 'csf_stl')
+
+        seg_pipe.connect(IsoSurface_tissues_pipe, "outputnode.wm_stl",
+                         outputnode, 'wm_stl')
+
+        seg_pipe.connect(IsoSurface_tissues_pipe, "outputnode.gm_stl",
+                         outputnode, 'gm_stl')
+
     return seg_pipe
 
 

macapype/pipelines/rename.py

@@ -470,20 +470,20 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe,
 
             print("Renaming wmgm_stl file")
 
-            rename_stereo_wmgm_stl = pe.Node(
-                niu.Rename(), name="rename_stereo_wmgm_stl")
-            rename_stereo_wmgm_stl.inputs.format_string = \
+            rename_csfwmgm_stl = pe.Node(
+                niu.Rename(), name="rename_csfwmgm_stl")
+            rename_csfwmgm_stl.inputs.format_string = \
                 pref_deriv + "_desc-wmgm_mask"
-            rename_stereo_wmgm_stl.inputs.parse_string = parse_str
-            rename_stereo_wmgm_stl.inputs.keep_ext = True
+            rename_csfwmgm_stl.inputs.parse_string = parse_str
+            rename_csfwmgm_stl.inputs.keep_ext = True
 
             main_workflow.connect(
                 segment_pnh_pipe, 'outputnode.wmgm_stl',
-                rename_stereo_wmgm_stl, 'in_file')
+                rename_csfwmgm_stl, 'in_file')
 
             main_workflow.connect(
-                rename_stereo_wmgm_stl, 'out_file',
-                datasink, '@stereo_wmgm_stl')
+                rename_csfwmgm_stl, 'out_file',
+                datasink, '@csfwmgm_stl')
 
             print("Renaming wmgm_nii file")
             rename_stereo_wmgm_mask = pe.Node(
@@ -501,6 +501,59 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe,
                 rename_stereo_wmgm_mask, 'out_file',
                 datasink, '@stereo_wmgm_mask')
 
+        if "IsoSurface_tissues_pipe" in params["brain_segment_pipe"]:
+
+            print("Renaming csf_stl file")
+
+            rename_csf_stl = pe.Node(
+                niu.Rename(), name="rename_csf_stl")
+            rename_csf_stl.inputs.format_string = \
+                pref_deriv + "_desc-csf_mask"
+            rename_csf_stl.inputs.parse_string = parse_str
+            rename_csf_stl.inputs.keep_ext = True
+
+            main_workflow.connect(
+                segment_pnh_pipe, 'outputnode.csf_stl',
+                rename_csf_stl, 'in_file')
+
+            main_workflow.connect(
+                rename_csf_stl, 'out_file',
+                datasink, '@csf_stl')
+
+            print("Renaming wm_stl file")
+
+            rename_wm_stl = pe.Node(
+                niu.Rename(), name="rename_wm_stl")
+            rename_wm_stl.inputs.format_string = \
+                pref_deriv + "_desc-wm_mask"
+            rename_wm_stl.inputs.parse_string = parse_str
+            rename_wm_stl.inputs.keep_ext = True
+
+            main_workflow.connect(
+                segment_pnh_pipe, 'outputnode.wm_stl',
+                rename_wm_stl, 'in_file')
+
+            main_workflow.connect(
+                rename_wm_stl, 'out_file',
+                datasink, '@wm_stl')
+
+            print("Renaming gm_stl file")
+
+            rename_gm_stl = pe.Node(
+                niu.Rename(), name="rename_gm_stl")
+            rename_gm_stl.inputs.format_string = \
+                pref_deriv + "_desc-gm_mask"
+            rename_gm_stl.inputs.parse_string = parse_str
+            rename_gm_stl.inputs.keep_ext = True
+
+            main_workflow.connect(
+                segment_pnh_pipe, 'outputnode.gm_stl',
+                rename_gm_stl, 'in_file')
+
+            main_workflow.connect(
+                rename_gm_stl, 'out_file',
+                datasink, '@gm_stl')
+
     elif "old_segment_pipe" in params.keys():
 
         if "mask_from_seg_pipe" in params.keys():

macapype/pipelines/surface.py

@@ -710,7 +710,7 @@ def create_IsoSurface_brain_pipe(params={},
                                output_names=["mask_file"],
                                function=merge_tissues),
         params=parse_key(params, "merge_brain_tissues"),
-        name="keep_GCC_brain")
+        name="merge_brain_tissues")
 
     IsoSurface_brain_pipe.connect(inputnode, 'segmented_file',
                                   merge_brain_tissues, 'dseg_file')
@@ -744,3 +744,54 @@ def create_IsoSurface_brain_pipe(params={},
                                   outputnode, "wmgm_stl")
 
     return IsoSurface_brain_pipe
+
+
+def create_IsoSurface_tissues_pipe(params={},
+                                   name="IsoSurface_tissues_pipe"):
+
+    # creating pipeline
+    IsoSurface_tissues_pipe = pe.Workflow(name=name)
+
+    # creating inputnode
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=["threshold_csf", "threshold_wm", "threshold_gm"]),
+        name='inputnode')
+
+    # csf2mesh
+    csf2mesh = pe.Node(interface=IsoSurface(),
+                       name="csf2mesh")
+
+    IsoSurface_tissues_pipe.connect(inputnode, 'threshold_csf',
+                                    csf2mesh, "nii_file")
+
+    # wm2mesh
+    wm2mesh = pe.Node(interface=IsoSurface(),
+                      name="wm2mesh")
+
+    IsoSurface_tissues_pipe.connect(inputnode, 'threshold_wm',
+                                    wm2mesh, "nii_file")
+
+    # gm2mesh
+    gm2mesh = pe.Node(interface=IsoSurface(),
+                      name="gm2mesh")
+
+    IsoSurface_tissues_pipe.connect(inputnode, 'threshold_gm',
+                                    gm2mesh, "nii_file")
+
+    # outputnode
+    outputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=["csf_stl", "gm_stl", "wm_stl"]),
+        name='outputnode')
+
+    IsoSurface_tissues_pipe.connect(csf2mesh, 'stl_file',
+                                    outputnode, "csf_stl")
+
+    IsoSurface_tissues_pipe.connect(wm2mesh, 'stl_file',
+                                    outputnode, "wm_stl")
+
+    IsoSurface_tissues_pipe.connect(gm2mesh, 'stl_file',
+                                    outputnode, "gm_stl")
+
+    return IsoSurface_tissues_pipe