Fixing ccs options brain masking

CHANGELOG.md

@@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Switch `sink_native_transforms` under `registration_workflows` to output all `.mat` files in ANTs and FSL Transforms.
 - `deoblique` field in pipeline config with `warp` and `refit` options to apply `3dWarp` or `3drefit` during data initialization.
 - `organism` configuration option.
+- Functionality to convert `space-T1w_desc-loose_brain_mask` and `space-T1w_desc-tight_brain_mask` into generic brain mask `space-T1w_desc-brain_mask` to use in brain extraction nodeblock downstream.
 
 ### Changed
 

CPAC/anat_preproc/anat_preproc.py

@@ -1303,7 +1303,7 @@
     # fslmaths tmp_mask.nii.gz -mas ${CCSDIR}/templates/MNI152_T1_1mm_first_brain_mask.nii.gz tmp_mask.nii.gz
     apply_mask = pe.Node(interface=fsl.maths.ApplyMask(), name=f"apply_mask_{node_id}")
 
-    wf.connect(skullstrip, "out_file", apply_mask, "in_file")
+    wf.connect(skullstrip, "mask_file", apply_mask, "in_file")
 
     node, out = strat_pool.get_data("T1w-brain-template-mask-ccs")
     wf.connect(node, out, apply_mask, "mask_file")
@@ -1347,36 +1347,18 @@
 
     wf.connect(combine_mask, "out_file", binarize_combined_mask, "in_file")
 
-    # CCS brain mask is in FS space, transfer it back to native T1 space
-    fs_fsl_brain_mask_to_native = pe.Node(
-        interface=freesurfer.ApplyVolTransform(),
-        name=f"fs_fsl_brain_mask_to_native_{node_id}",
-    )
-    fs_fsl_brain_mask_to_native.inputs.reg_header = True
-    fs_fsl_brain_mask_to_native.inputs.interp = "nearest"
-
-    wf.connect(
-        binarize_combined_mask, "out_file", fs_fsl_brain_mask_to_native, "source_file"
-    )
-
-    node, out = strat_pool.get_data("pipeline-fs_raw-average")
-    wf.connect(node, out, fs_fsl_brain_mask_to_native, "target_file")
-
-    node, out = strat_pool.get_data("freesurfer-subject-dir")
-    wf.connect(node, out, fs_fsl_brain_mask_to_native, "subjects_dir")
-
     if opt == "FreeSurfer-BET-Tight":
         outputs = {
             "space-T1w_desc-tight_brain_mask": (
-                fs_fsl_brain_mask_to_native,
-                "transformed_file",
+                binarize_combined_mask,
+                "out_file",
             )
         }
     elif opt == "FreeSurfer-BET-Loose":
         outputs = {
             "space-T1w_desc-loose_brain_mask": (
-                fs_fsl_brain_mask_to_native,
-                "transformed_file",
+                binarize_combined_mask,
+                "out_file",
             )
         }
 
@@ -2058,11 +2040,21 @@
         "T1w-brain-template-mask-ccs",
         "T1w-ACPC-template",
     ],
-    outputs=["space-T1w_desc-tight_brain_mask"],
+    outputs={
+        "space-T1w_desc-brain_mask": {
+            "Description": "Brain mask extracted using FreeSurfer-BET-Tight method",
+            "Method": "FreeSurfer-BET-Tight",
+            "Threshold": "tight",
+        }
+    },
 )
 def brain_mask_freesurfer_fsl_tight(wf, cfg, strat_pool, pipe_num, opt=None):
     wf, outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
 
+    # Convert the tight brain mask to generic brain mask
+    outputs["space-T1w_desc-brain_mask"] = outputs.pop(
+        "space-T1w_desc-tight_brain_mask"
+    )
     return (wf, outputs)
 
 
@@ -2107,11 +2099,21 @@
         "T1w-brain-template-mask-ccs",
         "T1w-ACPC-template",
     ],
-    outputs=["space-T1w_desc-loose_brain_mask"],
+    outputs={
+        "space-T1w_desc-brain_mask": {
+            "Description": "Brain mask extracted using FreeSurfer-BET-Loose method",
+            "Method": "FreeSurfer-BET-Loose",
+            "Threshold": "loose",
+        }
+    },
 )
 def brain_mask_freesurfer_fsl_loose(wf, cfg, strat_pool, pipe_num, opt=None):
     wf, outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
 
+    # Convert the loose brain mask to generic brain mask
+    outputs["space-T1w_desc-brain_mask"] = outputs.pop(
+        "space-T1w_desc-loose_brain_mask"
+    )
     return (wf, outputs)
 
 

CPAC/anat_preproc/tests/test_anat_preproc.py

@@ -5,6 +5,11 @@
 import nibabel as nib
 
 from .. import anat_preproc
+from unittest.mock import Mock, patch
+from ..anat_preproc import (
+    brain_mask_freesurfer_fsl_loose,
+    brain_mask_freesurfer_fsl_tight,
+)
 
 
 class TestAnatPreproc:
@@ -269,3 +274,71 @@ def test_anat_brain(self):
             # print 'correlation: ', correlation
 
             assert correlation[0, 1] >= 0.97
+
+
+@patch("CPAC.anat_preproc.anat_preproc.freesurfer_fsl_brain_connector")
+def test_brain_mask_freesurfer_fsl_loose(mock_connector):
+    """Test that brain_mask_freesurfer_fsl_loose correctly renames output key."""
+
+    mock_wf = Mock()
+    mock_cfg = Mock()
+    mock_strat_pool = Mock()
+    pipe_num = 1
+
+    mock_outputs = {
+        "space-T1w_desc-loose_brain_mask": "brain_mask_data",
+        "other_output": "other_data",
+    }
+
+    mock_connector.return_value = (mock_wf, mock_outputs)
+
+    result_wf, result_outputs = brain_mask_freesurfer_fsl_loose(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num
+    )
+
+    mock_connector.assert_called_once_with(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num, None
+    )
+
+    # Assert workflow returned unchanged
+    assert result_wf == mock_wf
+
+    # Assert output key was renamed correctly
+    assert "space-T1w_desc-brain_mask" in result_outputs
+    assert "space-T1w_desc-loose_brain_mask" not in result_outputs
+    assert result_outputs["space-T1w_desc-brain_mask"] == "brain_mask_data"
+    assert result_outputs["other_output"] == "other_data"
+
+
+@patch("CPAC.anat_preproc.anat_preproc.freesurfer_fsl_brain_connector")
+def test_brain_mask_freesurfer_fsl_tight(mock_connector):
+    """Test that brain_mask_freesurfer_fsl_tight correctly renames output key."""
+
+    mock_wf = Mock()
+    mock_cfg = Mock()
+    mock_strat_pool = Mock()
+    pipe_num = 1
+
+    mock_outputs = {
+        "space-T1w_desc-tight_brain_mask": "brain_mask_data",
+        "other_output": "other_data",
+    }
+
+    mock_connector.return_value = (mock_wf, mock_outputs)
+
+    result_wf, result_outputs = brain_mask_freesurfer_fsl_tight(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num
+    )
+
+    mock_connector.assert_called_once_with(
+        mock_wf, mock_cfg, mock_strat_pool, pipe_num, None
+    )
+
+    # Assert workflow returned unchanged
+    assert result_wf == mock_wf
+
+    # Assert output key was renamed correctly
+    assert "space-T1w_desc-brain_mask" in result_outputs
+    assert "space-T1w_desc-tight_brain_mask" not in result_outputs
+    assert result_outputs["space-T1w_desc-brain_mask"] == "brain_mask_data"
+    assert result_outputs["other_output"] == "other_data"