Hi Andres,

those errors are probably not related (tkmedit tries to read an array of cortical surfaces that don't exist for the BEM analysis). I'm not sure what BEM mesh editing tools exist - maybe Matti knows?

cheers, Bruce

On Wed, 3 Mar 2010, Andres Felipe Salazar Gomez wrote:

Hello FreeSurfer users,

I am using a set of MNE commands (mne_watershed_bem and mne_flash_bem) that call respectively mri_watershed and mri_make_bem_surfaces to create the BEM surfaces. I am having problems when checking one of them, the inner_skull mesh, since in several subjects, when visualized on tkmedit, it appears to be going not along the edge of the gray matter but inside it, specially at the occipital lobe level.

Has anyone had a similar problem? How can the inner_skull file be modified?

I found an error log file with the following info but I do not know if it is related to the problem.

MRISreadVertexPosition(orig): could not open file $SUBJECTS_DIR/$SUBJECT/bem/flash/lh.orig MRISreadVertexPosition(pial): could not open file SUBJECTS_DIR/$SUBJECT/bem/flash/lh.pial

I appreciate any help in this matter.

Thank you,

-- Andrés