Better skull coreg

skullTo3d/pipelines/skull_pipe.py

@@ -2164,6 +2164,7 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}):
         name='outputnode')
 
     if "crop_CT" in params:
+
         print('crop_CT is in params')
 
         assert "args" in params["crop_CT"].keys(), \
@@ -2182,68 +2183,137 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}):
         skull_ct_pipe.connect(inputnode, 'ct',
                               crop_CT, 'in_file')
 
-    # align_ct_on_T1
-    align_ct_on_T1 = pe.Node(interface=RegAladin(),
-                             name="align_ct_on_T1")
+        align_ct_on_T1 = pe.Node(fsl.FLIRT(), name="align_ct_on_T1")
+        align_ct_on_T1.inputs.dof = 6
 
-    align_ct_on_T1.inputs.rig_only_flag = True
+        align_ct_on_T1.inputs.cost = 'normmi'
 
-    if "crop_CT" in params:
         skull_ct_pipe.connect(
             crop_CT, "roi_file",
-            align_ct_on_T1, "flo_file")
-    else:
+            align_ct_on_T1, 'in_file')
+
         skull_ct_pipe.connect(
-            inputnode, 'ct',
-            align_ct_on_T1, "flo_file")
+            inputnode, "stereo_T1",
+            align_ct_on_T1, 'reference')
 
-    skull_ct_pipe.connect(inputnode, "native_T1",
-                          align_ct_on_T1, "ref_file")
+        if "align_ct_on_T1_2" in params:
 
-    if "align_ct_on_T1_2" in params:
+            align_ct_on_T1_2 = pe.Node(fsl.FLIRT(), name="align_ct_on_T1_2")
+            align_ct_on_T1_2.inputs.dof = 6
 
-        # align_ct_on_T1
-        align_ct_on_T1_2 = pe.Node(interface=RegAladin(),
-                                   name="align_ct_on_T1_2")
+            align_ct_on_T1_2.inputs.cost = 'normmi'
 
-        align_ct_on_T1_2.inputs.rig_only_flag = True
+            skull_ct_pipe.connect(
+                crop_CT, "roi_file",
+                align_ct_on_T1_2, 'in_file')
 
-        skull_ct_pipe.connect(align_ct_on_T1, 'res_file',
-                              align_ct_on_T1_2, "flo_file")
+            skull_ct_pipe.connect(
+                inputnode, "stereo_T1",
+                align_ct_on_T1_2, 'reference')
 
-        skull_ct_pipe.connect(inputnode, "native_T1",
-                              align_ct_on_T1_2, "ref_file")
+            # initial matrix
+            skull_ct_pipe.connect(
+                align_ct_on_T1, "out_matrix_file",
+                align_ct_on_T1_2, 'in_matrix_file')
 
-    # align_ct_on_stereo_T1
-    align_ct_on_stereo_T1 = pe.Node(
-        interface=RegResample(pad_val=0.0),
-        name="align_ct_on_stereo_T1")
+        if "align_ct_on_T1_2" in params:
+            skull_ct_pipe.connect(
+                align_ct_on_T1_2, 'out_file',
+                outputnode, "stereo_ct")
 
-    if "align_ct_on_T1_2" in params:
-        skull_ct_pipe.connect(align_ct_on_T1_2, 'res_file',
-                              align_ct_on_stereo_T1, "flo_file")
+        else:
+            skull_ct_pipe.connect(
+                align_ct_on_T1, 'out_file',
+                outputnode, "stereo_ct")
 
     else:
-        skull_ct_pipe.connect(align_ct_on_T1, 'res_file',
-                              align_ct_on_stereo_T1, "flo_file")
 
-    skull_ct_pipe.connect(inputnode, 'native_to_stereo_trans',
-                          align_ct_on_stereo_T1, "trans_file")
+        # align_ct_on_T1
+        align_ct_on_T1 = pe.Node(
+            interface=RegAladin(),
+            name="align_ct_on_T1")
 
-    skull_ct_pipe.connect(inputnode, "stereo_T1",
-                          align_ct_on_stereo_T1, "ref_file")
-    # output node
-    skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file",
-                          outputnode, "stereo_ct")
+        align_ct_on_T1.inputs.rig_only_flag = True
+
+        if "crop_CT" in params:
+            skull_ct_pipe.connect(
+                crop_CT, "roi_file",
+                align_ct_on_T1, "flo_file")
+        else:
+            skull_ct_pipe.connect(
+                inputnode, 'ct',
+                align_ct_on_T1, "flo_file")
+
+        skull_ct_pipe.connect(
+            inputnode, "native_T1",
+            align_ct_on_T1, "ref_file")
+
+        if "align_ct_on_T1_2" in params:
+
+            # align_ct_on_T1
+            align_ct_on_T1_2 = pe.Node(
+                interface=RegAladin(),
+                name="align_ct_on_T1_2")
+
+            align_ct_on_T1_2.inputs.rig_only_flag = True
+
+            skull_ct_pipe.connect(
+                align_ct_on_T1, 'res_file',
+                align_ct_on_T1_2, "flo_file")
+
+            skull_ct_pipe.connect(
+                inputnode, "native_T1",
+                align_ct_on_T1_2, "ref_file")
+
+        # align_ct_on_stereo_T1
+        align_ct_on_stereo_T1 = pe.Node(
+            interface=RegResample(pad_val=0.0),
+            name="align_ct_on_stereo_T1")
+
+        if "align_ct_on_T1_2" in params:
+            skull_ct_pipe.connect(
+                align_ct_on_T1_2, 'res_file',
+                align_ct_on_stereo_T1, "flo_file")
+
+        else:
+            skull_ct_pipe.connect(
+                align_ct_on_T1, 'res_file',
+                align_ct_on_stereo_T1, "flo_file")
+
+        skull_ct_pipe.connect(
+            inputnode, 'native_to_stereo_trans',
+            align_ct_on_stereo_T1, "trans_file")
+
+        skull_ct_pipe.connect(
+            inputnode, "stereo_T1",
+            align_ct_on_stereo_T1, "ref_file")
+
+        # output node
+        skull_ct_pipe.connect(
+            align_ct_on_stereo_T1, "out_file",
+            outputnode, "stereo_ct")
 
     if "skullmask_ct_pipe" in params:
 
         skullmask_ct_pipe = _create_skullmask_ct_pipe(
             name="skullmask_ct_pipe",
             params=params["skullmask_ct_pipe"])
 
-        skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file",
-                              skullmask_ct_pipe, "inputnode.realigned_ct")
+        if "crop_CT" in params:
+
+            if "align_ct_on_T1_2" in params:
+                skull_ct_pipe.connect(
+                    align_ct_on_T1_2, 'out_file',
+                    skullmask_ct_pipe, "inputnode.realigned_ct")
+
+            else:
+                skull_ct_pipe.connect(
+                    align_ct_on_T1, 'out_file',
+                    skullmask_ct_pipe, "inputnode.realigned_ct")
+        else:
+
+            skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file",
+                                  skullmask_ct_pipe, "inputnode.realigned_ct")
 
         skull_ct_pipe.connect(inputnode, "indiv_params",
                               skullmask_ct_pipe, "inputnode.indiv_params")

workflows/params_segment_macaque_0p5_ants_4animal_skull.json

@@ -87,6 +87,14 @@
     {
         "headmask_t1_pipe":
         {
+            "t1_head_auto_mask":
+            {
+                "kmeans": true,
+                "operation": "lower",
+                "index": 2,
+                "sample_bins": 30,
+                "distance": 10
+            },
             "t1_head_dilate":
             {
                 "operation": "modal",
@@ -114,17 +122,6 @@
                 "kernel_shape": "boxv",
                 "kernel_size": 9.0
             },
-            "t1_skull_gcc_erode":
-            {
-                "kernel_shape": "boxv",
-                "kernel_size": 5.0
-            },
-            "t1_skull_gcc_dilate":
-            {
-                "operation": "modal",
-                "kernel_shape": "boxv",
-                "kernel_size": 5.0
-            },
             "t1_skull_dilate":
             {
                 "operation": "modal",
@@ -140,6 +137,29 @@
             {
                 "brainsize": 45
             }
+        },
+
+
+        "fullskullmask_t1_pipe":
+        {
+            "brainmask_expand":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 11
+            },
+
+            "fullskull_dilate":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            },
+            "fullskull_erode":
+            {
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            }
         }
     },
     "skull_petra_pipe":
@@ -202,6 +222,28 @@
             {
                 "brainsize": 45
             }
+        },
+
+        "fullskullmask_petra_pipe":
+        {
+            "brainmask_expand":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 11
+            },
+
+            "fullskull_dilate":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            },
+            "fullskull_erode":
+            {
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            }
         }
     },
 
@@ -211,6 +253,32 @@
         {
         },
         "skullmask_ct_pipe":
+        {
+            "ct_skull_auto_mask":
+            {
+                "kmeans": true,
+                "sample_bins": 30,
+                "distance": 10,
+                "operation": "lower",
+                "index": 2
+            },
+            "ct_skull_dilate":
+            {
+                "operation" : "modal",
+                "kernel_shape" : "boxv",
+                "kernel_size" : 3.0
+            },
+            "ct_skull_erode":
+            {
+                "kernel_shape" : "boxv",
+                "kernel_size" : 3.0
+            },
+            "ct_skull_fov":
+            {
+                "brainsize" : 45
+            }
+        },
+        "skullmask_ct_pipe":
         {
             "ct_skull_auto_mask":
             {

workflows/params_segment_macaque_0p5_ants_4animal_skullnoisypetra.json

@@ -87,6 +87,14 @@
     {
         "headmask_t1_pipe":
         {
+            "t1_head_auto_mask":
+            {
+                "kmeans": true,
+                "operation": "lower",
+                "index": 2,
+                "sample_bins": 30,
+                "distance": 10
+            },
             "t1_head_dilate":
             {
                 "operation": "modal",
@@ -139,6 +147,28 @@
             {
                 "brainsize": 45
             }
+        },
+
+        "fullskullmask_t1_pipe":
+        {
+            "brainmask_expand":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 11
+            },
+
+            "fullskull_dilate":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            },
+            "fullskull_erode":
+            {
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            }
         }
     },
     "skull_petra_pipe":
@@ -213,6 +243,29 @@
             {
                 "brainsize": 45
             }
+        },
+
+
+        "fullskullmask_petra_pipe":
+        {
+            "brainmask_expand":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 11
+            },
+
+            "fullskull_dilate":
+            {
+                "operation": "modal",
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            },
+            "fullskull_erode":
+            {
+                "kernel_shape": "boxv",
+                "kernel_size": 7.0
+            }
         }
     },