Petra itk debias optional (#29)

optional petra_itk_debias for marmoset only
Macatools · Dec 13, 2024 · b313f46 · b313f46
1 parent 5db30fe
commit b313f46
Show file tree

Hide file tree

Showing 3 changed files with 52 additions and 19 deletions.
diff --git a/examples_doc/params_skull.json b/examples_doc/params_skull.json
@@ -109,6 +109,14 @@
 
     "skull_ct_pipe":
     {
+        "align_ct_on_T1_2":
+        {
+
+            "comment": "OPTIONAL",
+            "comment": "Cannot be modified",
+            "params": "RegAladin (NiftyReg)"
+
+        },
         "ct_head_mask_thr":
         {
             "params": "Threshold (FSL)",
@@ -149,12 +157,18 @@
 
         "avg_reorient_pipe":
         {
-
             "comment": "OPTIONAL",
             "params": "see corresponding doc in short_preparation_pipe in macapype"
 
         },
 
+        "petra_itk_debias":
+        {
+            "comment": "OPTIONAL",
+            "params": "SimpleITK N4BiasFieldCorrectionImageFilter dirty wrap (defined in macapype.nodes.correc_bias)",
+            "comment": "Should be made a proper nipype node ",
+
+        },
 
         "petra_head_mask_thr":
         {

diff --git a/skullTo3d/pipelines/skull_pipe.py b/skullTo3d/pipelines/skull_pipe.py
@@ -682,17 +682,18 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
     skull_petra_pipe.connect(inputnode, "stereo_T1",
                              align_petra_on_stereo_T1, "ref_file")
 
-    # Adding early petra_debias
-    petra_itk_debias = NodeParams(
-            interface=niu.Function(
-                input_names=["img_file"],
-                output_names=["cor_img_file", "bias_img_file"],
-                function=itk_debias),
-            params=parse_key(params, "petra_itk_debias"),
-            name="petra_itk_debias")
-
-    skull_petra_pipe.connect(align_petra_on_stereo_T1, "out_file",
-                             petra_itk_debias, "img_file")
+    if "petra_itk_debias" in params.keys():
+
+        # Adding early petra_debias
+        petra_itk_debias = pe.Node(
+                interface=niu.Function(
+                    input_names=["img_file"],
+                    output_names=["cor_img_file", "bias_img_file"],
+                    function=itk_debias),
+                name="petra_itk_debias")
+
+        skull_petra_pipe.connect(align_petra_on_stereo_T1, "out_file",
+                                 petra_itk_debias, "img_file")
 
     # ### head mask
     # headmask_threshold
@@ -703,8 +704,14 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
             params=parse_key(params, 'petra_head_mask_thr'),
             name="petra_head_mask_thr")
 
-        skull_petra_pipe.connect(petra_itk_debias, "cor_img_file",
-                                 petra_head_mask_thr, "in_file")
+        if "petra_itk_debias" in params.keys():
+
+            skull_petra_pipe.connect(petra_itk_debias, "cor_img_file",
+                                     petra_head_mask_thr, "in_file")
+        else:
+
+            skull_petra_pipe.connect(align_petra_on_stereo_T1, "out_file",
+                                     petra_head_mask_thr, "in_file")
 
         skull_petra_pipe.connect(
             inputnode, ('indiv_params', parse_key, "petra_head_mask_thr"),
@@ -720,8 +727,14 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
                 params=parse_key(params, "petra_head_auto_mask"),
                 name="petra_head_auto_mask")
 
-        skull_petra_pipe.connect(petra_itk_debias, "cor_img_file",
-                                 petra_head_auto_mask, "img_file")
+        if "petra_itk_debias" in params.keys():
+
+            skull_petra_pipe.connect(petra_itk_debias, "cor_img_file",
+                                     petra_head_auto_mask, "img_file")
+        else:
+
+            skull_petra_pipe.connect(align_petra_on_stereo_T1, "out_file",
+                                     petra_head_auto_mask, "img_file")
 
         skull_petra_pipe.connect(
             inputnode, ('indiv_params', parse_key, "petra_head_auto_mask"),
@@ -791,8 +804,14 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
     petra_hmasked = pe.Node(interface=ApplyMask(),
                             name="petra_hmasked")
 
-    skull_petra_pipe.connect(petra_itk_debias, "cor_img_file",
-                             petra_hmasked, "in_file")
+    if "petra_itk_debias" in params.keys():
+
+        skull_petra_pipe.connect(petra_itk_debias, "cor_img_file",
+                                 petra_hmasked, "in_file")
+    else:
+
+        skull_petra_pipe.connect(align_petra_on_stereo_T1, "out_file",
+                                 petra_hmasked, "in_file")
 
     skull_petra_pipe.connect(petra_head_erode, "out_file",
                              petra_hmasked, "mask_file")

diff --git a/workflows/params_segment_marmo_ants_skull.json b/workflows/params_segment_marmo_ants_skull.json
@@ -98,7 +98,7 @@
         }
     },
     "skull_petra_pipe":
-    {
+    {   "petra_itk_debias":{},
         "petra_head_auto_mask":
         {
             "kmeans": true,