[FIX] serialize numpy arrays to list before saving to json

doc/changes/latest.rst

@@ -18,6 +18,9 @@ Fixes
 - :bdg-dark:`Code` Masker reports tables do not overlap with report image (:gh:`4308` by `Rémi Gau`_).
 
 - :bdg-dark:`Code` Fix color bar handling with color map with only 1 level (:gh:`4255` by `Rémi Gau`_).
+
+- :bdg-dark:`Code` Ensure that :func:`nilearn.interfaces.bids.save_glm_to_bids` serializes numpy arrays to :obj:`list` used as GLM parameters before saving them to JSON (:gh:`4325` by `Rémi Gau`_).
+
 - :bdg-dark:`Code` Check that the ``view`` parameter in surface plotting functions is a pair of ``int`` or ``float`` when it is not a ``string`` (:gh:`4297` by `Rémi Gau`_).
 - :bdg-dark:`Code` Fix positions of the markers on the images on the sphere masker reports (:gh:`4285` by `Rémi Gau`_).
 - :bdg-dark:`Code` Fix cut position in nifti maps maskers to match displayed map maximum (:gh:`4304` by `Rémi Gau`_).

nilearn/interfaces/bids/glm.py

@@ -114,6 +114,10 @@
         ATTRIBUTE_RENAMING.get(k, k): v for k, v in model_attributes.items()
     }
 
+    for key, value in model_attributes.items():
+        if isinstance(value, (np.ndarray)):
+            model_attributes[key] = value.tolist()
+
     model_metadata = {
         "Description": "A statistical map generated by Nilearn.",
         **data_attributes,

nilearn/interfaces/tests/test_bids.py

@@ -342,15 +342,11 @@ def test_save_glm_to_bids(tmp_path_factory):
     ]
 
     shapes, rk = [(7, 8, 9, 15)], 3
-    mask, fmri_data, design_matrices = generate_fake_fmri_data_and_design(
+    _, fmri_data, design_matrices = generate_fake_fmri_data_and_design(
         shapes,
         rk,
     )
 
-    masker = NiftiMasker(mask)
-    masker.fit()
-
-    # Call with verbose (improve coverage)
     single_run_model = FirstLevelModel(
         mask_img=None,
         minimize_memory=False,
@@ -378,6 +374,40 @@ def test_save_glm_to_bids(tmp_path_factory):
         assert os.path.isfile(full_filename)
 
 
+def test_save_glm_to_bids_serialize_affine(tmp_path):
+    """Test that affines are turned into a serializable type.
+
+    Regression test for https://github.com/nilearn/nilearn/issues/4324.
+    """
+    shapes, rk = [(7, 8, 9, 15)], 3
+    mask, fmri_data, design_matrices = generate_fake_fmri_data_and_design(
+        shapes,
+        rk,
+    )
+
+    target_affine = mask.affine
+
+    single_run_model = FirstLevelModel(
+        target_affine=target_affine,
+        minimize_memory=False,
+    ).fit(
+        fmri_data[0],
+        design_matrices=design_matrices[0],
+    )
+
+    save_glm_to_bids(
+        model=single_run_model,
+        contrasts={
+            "effects of interest": np.eye(rk),
+        },
+        contrast_types={
+            "effects of interest": "F",
+        },
+        out_dir=tmp_path,
+        prefix="sub-01_ses-01_task-nback",
+    )
+
+
 @pytest.fixture
 def nb_cols_design_matrix():
     return 3