[DOC] Improve warnings for BIDS folders

nilearn/glm/first_level/first_level.py

@@ -1268,6 +1268,8 @@ def first_level_from_bids(
         derivatives_folder=derivatives_folder,
     )
 
+    dataset_path = Path(dataset_path).absolute()
+
     kwargs_load_confounds = _check_kwargs_load_confounds(**kwargs)
 
     if drift_model is not None and kwargs_load_confounds is not None:
@@ -1286,6 +1288,7 @@ def first_level_from_bids(
             )
 
     derivatives_path = Path(dataset_path) / derivatives_folder
+    derivatives_path = derivatives_path.absolute()
 
     # Get metadata for models.
     #
@@ -1325,17 +1328,19 @@ def first_level_from_bids(
         t_r = inferred_t_r
     if t_r is not None and t_r != inferred_t_r:
         warn(
-            f"'t_r' provided ({t_r}) is different "
+            f"\n't_r' provided ({t_r}) is different "
             f"from the value found in the BIDS dataset ({inferred_t_r}).\n"
-            "Note this may lead to the wrong model specification."
+            "Note this may lead to the wrong model specification.",
+            stacklevel=2,
         )
     if t_r is not None:
         _check_repetition_time(t_r)
     else:
         warn(
-            "'t_r' not provided and cannot be inferred from BIDS metadata.\n"
+            "\n't_r' not provided and cannot be inferred from BIDS metadata.\n"
             "It will need to be set manually in the list of models, "
-            "otherwise their fit will throw an exception."
+            "otherwise their fit will throw an exception.",
+            stacklevel=2,
         )
 
     # Slice time correction reference time
@@ -1394,6 +1399,8 @@ def first_level_from_bids(
     models_confounds = []
 
     sub_labels = _list_valid_subjects(derivatives_path, sub_labels)
+    if len(sub_labels) == 0:
+        raise RuntimeError(f"\nNo subject found in:\n {derivatives_path}")
     for sub_label_ in sub_labels:
         # Create model
         model = FirstLevelModel(
@@ -1494,8 +1501,10 @@ def _list_valid_subjects(derivatives_path, sub_labels):
             sub_labels_exist.append(sub_label_)
         else:
             warn(
-                f"Subject label {sub_label_} is not present in the"
-                " dataset and cannot be processed."
+                f"\nSubject label '{sub_label_}' is not present "
+                "in the following dataset and cannot be processed:\n"
+                f" {derivatives_path}",
+                stacklevel=3,
             )
 
     return set(sub_labels_exist)
@@ -1933,7 +1942,8 @@ def _make_bids_files_filter(
                     warn(
                         f"The filter {filter_} will be skipped. "
                         f"'{filter_[0]}' is not among the supported filters. "
-                        f"Allowed filters include: {supported_filters}"
+                        f"Allowed filters include: {supported_filters}",
+                        stacklevel=3,
                     )
                 continue
 

nilearn/glm/tests/test_first_level.py

@@ -1,7 +1,9 @@
 import itertools
 import os
+import shutil
 import unittest.mock
 import warnings
+from itertools import product
 from pathlib import Path
 
 import numpy as np
@@ -1461,10 +1463,7 @@ def test_first_level_from_bids_with_subject_labels(bids_dataset):
     Check that the incorrect label `foo` raises a warning,
     but that we still get a model for existing subject.
     """
-    warning_message = (
-        "Subject label foo is not present in"
-        " the dataset and cannot be processed"
-    )
+    warning_message = "Subject label 'foo' is not present in*"
     with pytest.warns(UserWarning, match=warning_message):
         models, *_ = first_level_from_bids(
             dataset_path=bids_dataset,
@@ -1854,9 +1853,6 @@ def test_missing_trial_type_column_warning(tmp_path_factory):
         )
 
 
-from itertools import product
-
-
 def test_first_level_from_bids_load_confounds(tmp_path):
     """Test that only a subset of confounds can be loaded."""
     n_sub = 2
@@ -1945,6 +1941,21 @@ def test_first_level_from_bids_load_confounds_warnings(tmp_path):
         )
 
 
+def test_first_level_from_bids_no_subject(tmp_path):
+    """Throw error when no subject found."""
+    bids_path = create_fake_bids_dataset(
+        base_dir=tmp_path, n_sub=1, n_ses=0, tasks=["main"], n_runs=[2]
+    )
+    shutil.rmtree(bids_path / "derivatives" / "sub-01")
+    with pytest.raises(RuntimeError, match="No subject found in:"):
+        first_level_from_bids(
+            dataset_path=bids_path,
+            task_label="main",
+            space_label="MNI",
+            slice_time_ref=None,
+        )
+
+
 def test_check_run_tables_errors():
     # check high level wrapper keeps behavior
     with pytest.raises(ValueError, match="len.* does not match len.*"):

nilearn/interfaces/bids/query.py

@@ -48,8 +48,8 @@ def _get_metadata_from_bids(
         else:
             warn(f"'{field}' not found in file {json_files[0]}.", stacklevel=3)
     else:
-        msg_suffix = f" in {bids_path}" if bids_path else ""
-        warn(f"No bold.json found in BIDS folder{msg_suffix}.")
+        msg_suffix = f" in:\n {bids_path}" if bids_path else ""
+        warn(f"\nNo bold.json found in BIDS folder{msg_suffix}.", stacklevel=3)
 
     return None
 
@@ -92,8 +92,11 @@ def infer_slice_timing_start_time_from_dataset(bids_path, filters, verbose=0):
     )
     if not img_specs:
         if verbose:
-            msg_suffix = f" in {bids_path}"
-            warn(f"No bold.json found in BIDS folder{msg_suffix}.")
+            msg_suffix = f" in:\n {bids_path}"
+            warn(
+                f"\nNo bold.json found in BIDS folder{msg_suffix}.",
+                stacklevel=3,
+            )
         return None
 
     return _get_metadata_from_bids(
@@ -137,8 +140,11 @@ def infer_repetition_time_from_dataset(bids_path, filters, verbose=0):
 
     if not img_specs:
         if verbose:
-            msg_suffix = f" in {bids_path}"
-            warn(f"No bold.json found in BIDS folder{msg_suffix}.")
+            msg_suffix = f" in:\n {bids_path}"
+            warn(
+                f"\nNo bold.json found in BIDS folder{msg_suffix}.",
+                stacklevel=3,
+            )
         return None
 
     return _get_metadata_from_bids(