getpwdcmd error in mne.bem.make_scalp_surfaces

[darcywaller]

I am receiving an error when running the make_scalp_surfaces function in a Jupyter notebook. The following command
mne.bem.make_scalp_surfaces(subject=subject,subjects_dir=subjects_dir,mri='T1.mgz')

outputs
1. Creating a dense scalp tessellation with mkheadsurf...
Running subprocess: mkheadsurf -subjid sub-104 -srcvol T1.mgz -thresh1 20 -thresh2 20
getpwdcmd: Command not found.

with the verbose error log displaying an error in run_subprocess that leads to
CalledProcessError: Command '['mkheadsurf', '-subjid', 'sub-104', '-srcvol', 'T1.mgz', '-thresh1', '20', '-thresh2', '20']' returned non-zero exit status 1..

Freesurfer is loaded with FREESURFER_HOME defined and subject and subjects_dir are certainly defined and do not generate errors when running mne.bem.make_flash_bem in the previous cell.

I'm running MNE version 1.8.0 and freesurfer version 7.3.2. Could you please advise what might be the issue?

[welcome]

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[larsoner]

Can you successfully run mkheadsurf --help on your system?

[darcywaller]

Yes! mkheadsurf --help is successfully returning the function documentation in the terminal and with ! in my jupyter notebook.

[shresth-keshari]

@darcywaller You're right that FREESURFER_HOME is set correctly, especially since mne.bem.make_flash_bem is working. However, make_scalp_surfaces specifically relies on mkheadsurf, which isn't used in make_flash_bem.

Try running the command directly in a terminal:
mkheadsurf -subjid sub-104 -srcvol T1.mgz -thresh1 20 -thresh2 20
If it works here but fails in Jupyter, the issue is with Jupyter’s environment.
If it fails here too, FreeSurfer itself may be misconfigured.

[darcywaller]

Running that full mkheadsurf command in both the terminal and the jupyter notebook still produces
getpwdcmd: Command not found.

I'm assuming this is a freesurfer bug and can work with my local IT team or freesurfer support (it's a Linux module I cannot change the version of) to try to resolve.