[FieldTrip] Error with ft_prepare_headmodel

[Kara Farrar]

Hi Everyone, 

When running ft_prepare_headmodel I have been getting the following error for a couple of participants: 
"Error using ft_prepare_headmodel (line 279) the compartment nesting cannot be determined”.
I have plotted the meshes (Brain, CSF, Skull, Scalp) for these participants (ft_plot_mesh), and it seems that the error only occurs for subjects where the scalp mesh appears to have the skull inside. 
I tried improving the contrast of the MRI on FSL (using fast -B <filename>), and running decouplesurf several times to check whether any of the layers are overlapping, but this hasn’t resolved the problem. I have also tried removing the indices where the skull and scalp overlap. However, this resulted in the scalp disappearing entirely, leaving only the skull behind.
I was wondering whether anyone had experienced similar issues? I have been unable to find anything similar online.  

Thank you in advance,

Kara

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