ValueError: Error loading surface from... ValueError: File does not appear to be a Freesurfer surface

PracticalMEEG2025
1

Continuing the discussion from [MNE-Python] Pr25 Participants instructions:

Hi,

Just starting this as a new thread. I too get the same error,

ValueError: Error loading surface from C:\Users\rampr\extra_data_mne\freesurfer\sub-01\bem\outer_skin.surf (see Terminal for details).

RuntimeError: The FREESURFER_HOME environment variable is not set.

after running,

subjects_dir = extra_path / “freesurfer”
mne.gui.coregistration(subject=‘sub-01’, subjects_dir=subjects_dir, inst=raw_fname);

I am using Jupyter Notebook on a Conda Env.

Ram.

@nschawor @wmvanvliet @christelle.guette

2

Hi!
I ran into the same issue.
From what I understand, the file itself is too small and seems to be missing the required information.
I noticed there’s another dataset in the folder called fsaverage (I assume it’s an average across participants).
Once I changed 'sub-01' to 'fsaverage' in the code, it worked for me :slight_smile:
I guess that for testing purposes, this should be good enough.

Orel

3

That file is a symbolic link. This will not work on windows. I’ll create a new version of extra_data_mne for you. For a quick fix execute:

from shutil import copyfile
for surface_name in ["brain", "inner_skull", "outer_skull", "outer_skin"]:
    copyfile(f"{extra_path}/freesurfer/sub-01/bem/watershed/sub-01_{surface_name}_surface",
             f"{extra_path}/freesurfer/sub-01/bem/{surface_name}.surf")
4

I’ve uploaded a new version of the extra data, now called extra_meg_data-v2.zip. See the updated README in the repo (either on github or do a git pull) for the link. Please let me know if the file is not publicly accessible for some reason.

5

Let’s keep the code snippet above in our back pocket for when we have participants who somehow ended up with the old mne_extra_data.zip file. Thanks for reporting this bug!