Fix TR in denoised NIfTI headers (#1038)

xcp_d/interfaces/nilearn.py

@@ -395,13 +395,19 @@ def _run_interface(self, runtime):
             "uncensored_denoised.nii.gz",
         )
         uncensored_denoised_img = masker.inverse_transform(uncensored_denoised_bold)
+        pixdim = list(uncensored_denoised_img.header.get_zooms())
+        pixdim[3] = self.inputs.TR
+        uncensored_denoised_img.header.set_zooms(pixdim)
         uncensored_denoised_img.to_filename(self._results["uncensored_denoised_bold"])
 
         self._results["interpolated_filtered_bold"] = os.path.join(
             runtime.cwd,
             "filtered_denoised.nii.gz",
         )
         filtered_denoised_img = masker.inverse_transform(interpolated_filtered_bold)
+        pixdim = list(filtered_denoised_img.header.get_zooms())
+        pixdim[3] = self.inputs.TR
+        filtered_denoised_img.header.set_zooms(pixdim)
         filtered_denoised_img.to_filename(self._results["interpolated_filtered_bold"])
 
         return runtime

xcp_d/tests/test_cli.py

@@ -197,7 +197,7 @@ def test_ukbiobank(data_dir, output_dir, working_dir):
         opts.work_dir,
         "dset_bids/derivatives/ukb",
     )
-    check_affines(converted_fmri_dir, out_dir, input_type="nifti")
+    check_affines(converted_fmri_dir, out_dir, input_type="ukb")
 
 
 @pytest.mark.pnc_cifti

xcp_d/tests/utils.py

@@ -122,7 +122,7 @@ def check_affines(data_dir, out_dir, input_type):
             extension=".dtseries.nii",
         )
 
-    elif input_type == "nifti":  # Get the .nii.gz
+    elif input_type in ("nifti", "ukb"):  # Get the .nii.gz
         # Problem: it's collecting native-space data
         denoised_files = xcp_layout.get(
             datatype="func",
@@ -155,17 +155,18 @@ def check_affines(data_dir, out_dir, input_type):
 
     preproc_file = preproc_files[0].path
     denoised_file = denoised_files[0].path
+    img1 = nb.load(preproc_file)
+    img2 = nb.load(denoised_file)
 
     if input_type == "cifti":
-        assert (
-            nb.load(preproc_file)._nifti_header.get_intent()
-            == nb.load(denoised_file)._nifti_header.get_intent()
-        )
+        assert img1._nifti_header.get_intent() == img2._nifti_header.get_intent()
+        np.testing.assert_array_equal(img1.nifti_header.get_zooms(), img2.nifti_header.get_zooms())
     else:
-        if not np.array_equal(nb.load(preproc_file).affine, nb.load(denoised_file).affine):
-            raise AssertionError(f"Affines do not match:\n\t{preproc_file}\n\t{denoised_file}")
-
-    print("No affines changed.")
+        np.testing.assert_array_equal(img1.affine, img2.affine)
+        if input_type != "ukb":
+            # The UK Biobank test dataset has the wrong TR in the header.
+            # I'll fix it at some point, but it's not the software's fault.
+            np.testing.assert_array_equal(img1.header.get_zooms(), img2.header.get_zooms())
 
 
 def run_command(command, env=None):