Fixing issue-13767

Author: 1himan

mne/stats/permutations.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from ..parallel import parallel_func
-from ..utils import check_random_state, logger, verbose
+from ..utils import _check_if_nan, check_random_state, logger, verbose
 
 
 def _max_stat(X, X2, perms, dof_scaling):
@@ -77,6 +77,7 @@ def permutation_t_test(
     """
     from .cluster_level import _get_1samp_orders
 
+    _check_if_nan(X)
     n_samples, n_tests = X.shape
     X2 = np.mean(X**2, axis=0)  # precompute moments
     mu0 = np.mean(X, axis=0)

mne/utils/check.py

@@ -699,10 +699,13 @@ def _path_like(item):
         return False
 
 
-def _check_if_nan(data, msg=" to be plotted"):
+def _check_if_nan(data, on_nan="error", msg=" to be plotted"):
     """Raise if any of the values are NaN."""
     if not np.isfinite(data).all():
-        raise ValueError(f"Some of the values {msg} are NaN.")
+        if on_nan == "error":
+            raise ValueError(f"Some of the values {msg} are NaN.")
+        elif on_nan == "warn":
+            warn(f"Some of the values {msg} are NaN")
 
 
 @verbose