Adding validation node for TR of bold outputs

FCP-INDI · Sep 11, 2024 · e848147 · e848147
1 parent a442aea
commit e848147
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Showing 2 changed files with 20 additions and 6 deletions.
diff --git a/CPAC/pipeline/engine.py b/CPAC/pipeline/engine.py
@@ -1357,7 +1357,7 @@ def gather_pipes(self, wf, cfg, all=False, add_incl=None, add_excl=None):
                 except OSError as os_error:
                     WFLOGGER.warning(os_error)
                     continue
-
+                
                 write_json_imports = ["import os", "import json"]
                 write_json = pe.Node(
                     Function(
@@ -1371,6 +1371,17 @@ def gather_pipes(self, wf, cfg, all=False, add_incl=None, add_excl=None):
                 write_json.inputs.json_data = json_info
 
                 wf.connect(id_string, "out_filename", write_json, "filename")
+
+                # Node to validate TR (and other scan parameters)
+                validate_bold_header = pe.Node(
+                    Function(
+                        input_names=["input_resource", "RawSource"],
+                        output_names=["output_resource"],
+                        function=validate_bold_header,
+                    ),
+                    name=f"validate_bold_header_{resource_idx}_{pipe_x}",
+                )
+
                 ds = pe.Node(DataSink(), name=f"sinker_{resource_idx}_{pipe_x}")
                 ds.inputs.parameterization = False
                 ds.inputs.base_directory = out_dct["out_dir"]

diff --git a/CPAC/pipeline/utils.py b/CPAC/pipeline/utils.py
@@ -52,19 +52,22 @@ def update_pixel_dim4(file_path, new_pixdim4):
 
 def validate_outputs(input_bold, RawSource_bold):
     """Match pixdim[4]/TR of the input_bold with RawSource_bold."""
-    input_pixdim4 = find_pixel_dim4(input_bold)
+
+    output_bold = input_bold
+    output_pixdim4 = find_pixel_dim4(output_bold)
     source_pixdim4 = find_pixel_dim4(RawSource_bold)
 
-    if input_pixdim4 != source_pixdim4:
+    if output_pixdim4 != source_pixdim4:
         print(f"TR mismatch detected between input_bold and RawSource_bold.")
-        print(f"input_bold TR: {input_pixdim4} seconds")
+        print(f"input_bold TR: {output_pixdim4} seconds")
         print(f"RawSource_bold TR: {source_pixdim4} seconds")
         print(f"Attempting to update the TR of input_bold to match RawSource_bold.")
-        update_pixel_dim4(input_bold, source_pixdim4)
+        update_pixel_dim4(output_bold, source_pixdim4)
     else:
         print(f"TR match detected between input_bold and RawSource_bold.")
-        print(f"input_bold TR: {input_pixdim4} seconds")
+        print(f"input_bold TR: {output_pixdim4} seconds")
         print(f"RawSource_bold TR: {source_pixdim4} seconds")
+    return output_bold
 
 def name_fork(resource_idx, cfg, json_info, out_dct):
     """Create and insert entities for forkpoints.