Use brain mask in NIFTI connectivity workflow (#733)

PennLINC · Dec 19, 2022 · 76ce7d7 · 76ce7d7
1 parent 786533d
commit 76ce7d7
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Showing 5 changed files with 40 additions and 9 deletions.
diff --git a/.circleci/tests/test_conn.py b/.circleci/tests/test_conn.py
@@ -53,6 +53,7 @@ def test_nifti_conn(fmriprep_with_freesurfer_data, tmp_path_factory):
     fcon_ts_wf.inputs.inputnode.t1w_to_native = t1w_to_native_xform
     fcon_ts_wf.inputs.inputnode.clean_bold = fake_bold_file
     fcon_ts_wf.inputs.inputnode.bold_file = bold_file
+    fcon_ts_wf.inputs.inputnode.bold_mask = bold_mask
     fcon_ts_wf.inputs.inputnode.ref_file = boldref
     fcon_ts_wf.base_dir = tmp_path_factory.mktemp("fcon_nifti_test_2")
     fcon_ts_wf.run()
@@ -86,7 +87,7 @@ def test_nifti_conn(fmriprep_with_freesurfer_data, tmp_path_factory):
     atlas = nb.load(atlas)
 
     # Masking img
-    masker = NiftiLabelsMasker(atlas, smoothing_fwhm=None, standardize=False)
+    masker = NiftiLabelsMasker(atlas, mask_img=bold_mask, smoothing_fwhm=None, standardize=False)
     # Fitting mask
     masker.fit(fake_bold_file)
     signals = masker.transform(fake_bold_file)

diff --git a/xcp_d/interfaces/connectivity.py b/xcp_d/interfaces/connectivity.py
@@ -29,6 +29,7 @@
 
 class _NiftiConnectInputSpec(BaseInterfaceInputSpec):
     filtered_file = File(exists=True, mandatory=True, desc="filtered file")
+    mask = File(exists=True, mandator=True, desc="brain mask file")
     atlas = File(exists=True, mandatory=True, desc="atlas file")
 
 
@@ -48,10 +49,16 @@ def _run_interface(self, runtime):
         # Then write out functional correlation matrix of
         # timeseries using numpy.
         self._results["time_series_tsv"] = fname_presuffix(
-            self.inputs.filtered_file, suffix="time_series.tsv", newpath=runtime.cwd, use_ext=False
+            self.inputs.filtered_file,
+            suffix="time_series.tsv",
+            newpath=runtime.cwd,
+            use_ext=False,
         )
         self._results["fcon_matrix_tsv"] = fname_presuffix(
-            self.inputs.filtered_file, suffix="fcon_matrix.tsv", newpath=runtime.cwd, use_ext=False
+            self.inputs.filtered_file,
+            suffix="fcon_matrix.tsv",
+            newpath=runtime.cwd,
+            use_ext=False,
         )
 
         (
@@ -60,6 +67,7 @@ def _run_interface(self, runtime):
         ) = extract_timeseries_funct(
             in_file=self.inputs.filtered_file,
             atlas=self.inputs.atlas,
+            mask=self.inputs.mask,
             timeseries=self._results["time_series_tsv"],
             fconmatrix=self._results["fcon_matrix_tsv"],
         )

diff --git a/xcp_d/utils/fcon.py b/xcp_d/utils/fcon.py
@@ -9,13 +9,15 @@
 from templateflow.api import get as get_template
 
 
-def extract_timeseries_funct(in_file, atlas, timeseries, fconmatrix):
+def extract_timeseries_funct(in_file, mask, atlas, timeseries, fconmatrix):
     """Use Nilearn NiftiLabelsMasker to extract timeseries.
 
     Parameters
     ----------
     in_file : str
         bold file timeseries
+    mask : str
+        BOLD file's associated brain mask file.
     atlas : str
         atlas in the same space with bold
     timeseries : str
@@ -30,9 +32,16 @@ def extract_timeseries_funct(in_file, atlas, timeseries, fconmatrix):
     fconmatrix : str
         functional connectivity matrix filename
     """
-    masker = NiftiLabelsMasker(labels_img=atlas, smoothing_fwhm=None, standardize=False)
+    masker = NiftiLabelsMasker(
+        labels_img=atlas,
+        mask_img=mask,
+        smoothing_fwhm=None,
+        standardize=False,
+    )
+
     # Use nilearn for time_series
     time_series = masker.fit_transform(in_file)
+
     # Use numpy for correlation matrix
     correlation_matrices = np.corrcoef(time_series.T)
 

diff --git a/xcp_d/workflow/bold.py b/xcp_d/workflow/bold.py
@@ -577,8 +577,11 @@ def init_boldpostprocess_wf(
 
     # functional connect workflow
     workflow.connect([
-        (downcast_data, fcon_ts_wf, [('bold_file', 'inputnode.bold_file'),
-                                     ('ref_file', 'inputnode.ref_file')]),
+        (downcast_data, fcon_ts_wf, [
+            ('bold_file', 'inputnode.bold_file'),
+            ("bold_mask", "inputnode.bold_mask"),
+            ('ref_file', 'inputnode.ref_file'),
+        ]),
         (inputnode, fcon_ts_wf, [('template_to_t1w', 'inputnode.template_to_t1w'),
                                  ('t1w_to_native', 'inputnode.t1w_to_native')]),
         (filtering_wf, fcon_ts_wf, [('filtered_file', 'inputnode.clean_bold')])

diff --git a/xcp_d/workflow/connectivity.py b/xcp_d/workflow/connectivity.py
@@ -77,7 +77,14 @@ def init_nifti_functional_connectivity_wf(
 
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["bold_file", "ref_file", "clean_bold", "template_to_t1w", "t1w_to_native"],
+            fields=[
+                "bold_file",
+                "bold_mask",
+                "ref_file",
+                "clean_bold",
+                "template_to_t1w",
+                "t1w_to_native",
+            ],
         ),
         name="inputnode",
     )
@@ -145,7 +152,10 @@ def init_nifti_functional_connectivity_wf(
                                                    ("template_to_t1w", "template_to_t1w"),
                                                    ("t1w_to_native", "t1w_to_native")]),
         (inputnode, warp_atlases_to_bold_space, [("ref_file", "reference_image")]),
-        (inputnode, nifti_connect, [("clean_bold", "filtered_file")]),
+        (inputnode, nifti_connect, [
+            ("clean_bold", "filtered_file"),
+            ("bold_mask", "mask"),
+        ]),
         (inputnode, matrix_plot, [("clean_bold", "in_file")]),
         (atlas_name_grabber, outputnode, [("atlas_names", "atlas_names")]),
         (atlas_name_grabber, atlas_file_grabber, [("atlas_names", "atlas_name")]),