External Email - Use Caution Hi everyone,
Can someone tell me if the 'surfs/*h.pial' surfaces generated in freesurfer and the surfaces generated by mne_watershed_bem/mri_watershed (i.e. 'bem/watershed/*brain_surface, 'bem/watershed/*inner_skull_surface', etc) are in the same co-ordinate systems? And if they are not in the exact same co-ordinate system, what transform is required to co-register the surfaces in the 'surfs' folder with the surfaces in the 'bem/watershed' folder? For a given subject, when I plot the *h.pial and *inner_skull_surface in freesurfer's freeview the brain sits nicely in the inner skull. When I plot the brain and inner skull in fieldtrip the brain surface crosses the inner skull. Therefore I am not sure if freesurfer's freeview has to do something to co-register *h.pial and *inner_skull_surface , or if something is going wrong in fieldtrip when loading in these two surfaces even though I use the exact same function to load them in (ft_read_headshape). I am using default scripting for running freesurfer and mne_watershed_bem (an mne script that runs mri_watershed) as can be seen in the file at this link: https://www.dropbox.com/s/znivq8cbc8c1959/sge_launch_freesurfer_mne_ants_all.sh?dl=0 Cheers, Levin Kuhlmann, PhD Centre for Human Psychopharmacology Swinburne University of Technology & Departments of Medicine and Biomedical Engineering The University of Melbourne. lkuhlm...@swin.edu.au<mailto:lkuhlm...@swin.edu.au> lev...@unimelb.edu.au<mailto:lev...@unimelb.edu.au> Ph: +61412 552283
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