[Mne_analysis] Crossing Segmentations

[dgw]

Hi Isaiah,

I can't see the crossing in the images (if you make the surfaces visible in
the 2d slice you can actually visualize all the places the surfaces cross
easier; especially, because you can see all three at once not just the
outermost), but I'll take your word for it. The bumps shouldn't be a
problem for doing the calculations, but I wonder whether you think they
exist in reality (how well does the surface line up with the skin surface
when moving through the 2d slices?). Unfortunately, the poor lower skull
coverage in your MRI will force you to either try some hacks to get
surfaces, which don't cross. (For future studies, you may want to make sure
to include all of the skull with maybe a little extra cushion space on top
of that).

The only way i can think of to try to make this work is to try to paint
(using tkmedit, or freeview) on a copy of the T1 extra material below to
give the surface production something else to latch onto. You might be able
to copy in matlab some data from the sample head if you can line up the
lower portions somewhat. These are very hacky solutions, but they are the
only ones which I can think of for this problem. Unfortunately, I'm
guessing your T1 doesn't have any cerebellum coverage, which is likely a
large part of the problem. You really, need an image which includes all of
the skull to fit surfaces around it well.

HTH,
D



On Wed, Aug 6, 2014 at 5:28 PM, Isaiah C. Smith <
Isaiah.C.Smith.17 at dartmouth.edu> wrote:

>
>  Hello All,
>
> Thank you for the help. I looked at my surface images in free view and
> they are crossing. The crossing seems to be taking place between the the
> brain and inner skull crossing over outer skull and outer skin. I believe
> that this is because the data that we have only goes down so far in the
> original mr images (Below). And when the individual surfaces are created
> they cross towards the posterior part of the head (Next Image). I attached
> the surfaces just in case to allow you to see. Would it be possible to
> extend outer skull and skin when using freesurfer, or get around this some
> other way. And lastly we are getting a very bumpy skin (Last Photo). Will
> this be a problem when creating the head model, finding the lead field
> matrix, etc. with MNE with MATLAB because the crossing sections prevent me
> from proceeding?
>
> Isaiah
>
>
>
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