Hi Levin
if you run mris_info on the surface files it should print out the matrices that freeview uses to compute a voxel coordinate from a surface vertex location. They are probably different for the BEM surfaces and the ?h.pial
cheers Bruce
On Thu, 21 Jun 2018, Levin Kuhlmann wrote:
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...
Cheers,
Levin Kuhlmann, PhD
Centre for Human Psychopharmacology
Swinburne University of Technology
&
Departments of Medicine and Biomedical Engineering
The University of Melbourne.
lkuhlmann@swin.edu.au
levink@unimelb.edu.au
Ph: +61412 552283