Dear all,

I would like an accurate segmentation of the brain without skull in native space. I am running a recon-all with Freesurfer 6 and Ubuntu 16.04. When it finishes, I find mistakes and I erase some skull voxels from brainmask.mgz. I run recon-all again and it finished without errors.

When I used to do that proccess with Freesurfer 5.1, I masked rawavg.mgz with brain.mgz to get the final segmented brain:

mri_mask rawavg.mgz brain.mgz brainraw.mgz

mri_convert -odt float brainraw.mgz brain.nii

In that case, deleted voxels are set to background in brain.mgz (my manual changes affect to brain.mgz). Now I am using Freesurfer 6 and my manual erased voxels appears in brain.mgz (they are not black). 

So, what output from Freesurfer should I use to the above goal? Should I use brain.finalsurfs.mgz? 

Thanks you in advance

M del Mar