[FieldTrip] Problems with meshes

[Kara Farrar]

Hi Everyone, 

I have been having three different problems with the meshes produced following segmentation, which has been preventing me from creating head models. I have attached screenshots of the mesh plots to better explain these problems. 

1) For several subjects the brain and scalp meshes appear correct, but the CSF and skull meshes are misshaped or broken. I have tried improving the contrast of the image on FSL (fast -B <filename>), and running decouplesurf several times to check whether any of the layers are overlapping, but this hasn’t fixed the problem.

2) For other subjects the brain, CSF, and skull meshes look correct but the scalp mesh shows the skull inside. When I then try running the ft_prepare_headmodel function I get the following error: "Error using ft_prepare_headmodel (line 279)
the compartment nesting cannot be determined”. I again tried improving the contrast but this didn’t help to remove the skull from inside of the scalp mesh. 

3) Finally, for one subject who's MRI image was an EEG-MRI, the skull and scalp meshes appear to be raised in the centre. Changing the image contrast again didn’t help to resolve this.

I was just wondering whether anyone else experienced similar issues to these, and if so how you were able to fix them? I have been unable to find any solutions online. 

Thank you in advance.

Best Wishes,

Kara 





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