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ENH: improve FreeSurfer error message when executable not found #13790

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ENH: improve FreeSurfer error message when executable not found #13790

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ENH: improve error message when FreeSurfer executable not found
ayuclan Mar 26, 2026
bcb8771
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 26, 2026
efcb22b
Merge branch 'main' into fix-freesurfer-error-message
ayuclan Mar 26, 2026
2ae67db
Update mne/bem.py
ayuclan Mar 30, 2026
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13 changes: 12 additions & 1 deletion mne/bem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1313,7 +1313,18 @@ def make_watershed_bem(
f"\nResults dir = {ws_dir}\nCommand = {' '.join(cmd)}\n"
)
os.makedirs(op.join(ws_dir))
run_subprocess_env(cmd)
try:
run_subprocess_env(cmd)
except FileNotFoundError:
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@wmvanvliet wmvanvliet Mar 31, 2026

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Suggested change
except FileNotFoundError:
except FileNotFoundError as e:

raise RuntimeError(
"FreeSurfer executable 'mri_watershed' not found.\n\n"
"This usually means FreeSurfer is not properly configured.\n"
"Make sure:\n"
"- FREESURFER_HOME is set\n"
"- $FREESURFER_HOME/bin is in your PATH\n"
"- You started Python/Jupyter from a terminal where SetupFreeSurfer.sh is sourced\n\n"
"See MNE installation documentation for details."
)
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@wmvanvliet wmvanvliet Mar 31, 2026

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Suggested change
)
) from e

del tempdir # clean up directory
if op.isfile(T1_mgz):
new_info = _extract_volume_info(T1_mgz)
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