bad skin (head shape) surface model in mne.gui.coregistration

Platform macOS-12.7.3-x86_64-i386-64bit
Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:35:23) [Clang 15.0.7 ]
Executable /Applications/.mne-python/bin/python
CPU i386 (4 cores)
Memory 8.0 GB

mne 1.6.0

simply running mne.gui.coregistration() with SUBJECTS_DIR set is sufficient
to get the coreg gui to pop up with the

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my message was not finished, as you can see the mri head shape/skin surface is very blurred and inacurate, not sufficient to accurately place the fiducials. the mri is of
good quality as is the freesurfer recon and the bem surfaces. The mri is from an MPnRAGE sequence and so the distribution and overall intensity levels may not
be the usual. It seems a threshold problem ? would not want to rerun the watershed as the bem surfaces are quite good. how to fix ?

thanks for any help


Can you try passing head_high_res=True to the coregistration() function?

that was quick, ill try as soon as i can and get back



Hi Richard, I added head_high_res=True and it had no effect, also it might be informative to tell you that when the loading is done the screen shows flat gray and when I scroll the head opacity all the way to the right at the very last bit the mri blob pops out of the gray background, so it seems the range is not as expected

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@larsoner Any idea what might be happening here?

IIRC head_high_res=True will try to use the high res head surface but won’t if it doesn’t exist – it might just fall back to using the one from the watershed BEM (which it looks like it’s using). Do you have $SUBJECTS_DIR/$SUBJECT/surf/lh.seghead? If not runninng mne make_scalp_surfaces or similar should create it