Hi Bruce,

Thank you for such a prompt reply.  The segmentation seems to have gone wrong due to the fact that white matter at the very front of the brain has voxel values significantly lower than 110 - I think this is due to intensity bias in the original image.  Thus in some slices the white matter is surrounded by red and considered a pial surface, with no white matter surface (yellow line) visible - see example attached. 

Having added control points to the white matter at the front of the brain and re-run recon-all the output is much better - is this ok ?  Am I right in thinking that GE acquisitions can have more problems with intensity bias than Siemens MPRAGE images ?

And finally when would one edit the wm.mgz volume - for example in this case could I have not filled in the white matter voxels which were misclassified anteriorly, though I guess it is more difficult to paint in the voxels especially where there is no segmentation at all.

Thanks.

M

PS Apologies if this is a re-posting but I was not sure if it made it to list

On Sun, Dec 4, 2011 at 4:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Mahinda

it depends on whether the frontal regions in the brainmask.mgz have intensities significantly lower than 110. Probably what you are seeing is incorrect topology fixing which is usually due to incorrect segmentation. The question is why is the segmentation incorrect.

cheers
Bruce


On Sun, 4 Dec 2011, Mahinda Yogarajah wrote:

Dear Freesurfer Experts,

I am processing some coronally acquired 3T GE FSPGR T1 volumes.  I have
noticed that on occasion slices pial and white surfaces at the very front of
the brain can go very wrong - either frontal slices are excluded all
together (present in brainmask.mgz but no pial or wm surfaces derived) or
white matter is mistakenly classified as grey matter. 

In order to correct this am I correct in assuming that the best method would
be to use control points to fix the intensity normalisation ? 
Alternatively, when is it better to edit the wm.mgz volume to include those
voxels which are white matter ? - It is not entirely clear to me from the
tutorial.

Thank you.

M




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