Hi Mark,
Many thanks. I got the coordinates and used these commands to create a spherical mask of radius 20mm:
fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi 127 1 168 1 110 1 0 1 mask_F3_point -odt float
fslmaths mask_F3_point -kernel sphere 20 -fmean mask_F3_sphere -odt float
A couple of issues:
1) My electrodes were 40x40mm squares, and as a first attempt, I'd like to have a mask that has this surface area (40x40mm) at the level of the cortex, and that in terms of depth goes all the way till the WM-GM border. I guess that, better than to start with a spherical mask, would be to start with a cubical (or rather: parallelepipedal) one, but how can I still control its centre point and the size of its 3 edges (40x40xcortex_depth)?
2) As you indicated previously, I understand that after creating the mask, it then needs to be multiplied with a BET mask to exclude non-brain voxels. Since I want the mask to extend all the way down into the cortex till the WM-GM border, I figured that multiplying with the "GM_mask" produced by FSLVBm would be best, as it also takes care of the out-of-brain problem.
However, GM_mask seems to include much more than just GM voxels: for instance, the space between sulcal walls corresponds to white voxels in GM_mask. That might be due to the insufficient 2mm resolution that I know is standard for masks used with FSLVBM, but still - is this the proper mask to multiply by?
3) I tried to see how the mask looks like with regard to the MNI template brain in the 3D Viewer, however the 3D viewer (opened from the Tools menu) is always blank. Both the mask and the underlying MNI template were visible from the layers menu. Is the 3D viewer not able to render such a scenario?
Many thanks!
Tudor