[Mne_analysis] MRI problem with head reconstruction

[Stephen Politzer-Ahles]

Hi Santosh,

What specifically is the problem with the outer skin?

I don't know if this is relevant for you, but when I did reconstructions I
ran into problems because my original MRIs had some high-density voxels
above the head, which watershed then interpreted as skull and tried to draw
the outer skin and outer skull around them (leaving what looked like a
mushroom on top of the subject's head); I fixed the problem by manually
erasing the bad voxels in Freesurfer using *tkmedit <subject> T1.mgz*.

Best,
Steve Politzer-Ahles

On Mon, Apr 2, 2012 at 11:15 AM, <santosh at nmr.mgh.harvard.edu> wrote:

> Hello,
>
>     I have a MRI subject, where once we performed reconstruction, the
> brain came out fine, but the outer skin was not properly
> reconstructed. I tried using mri_watershed to manually add control
> points in order to try to rectify this problem, with no luck. Here is
> the command.
>
>
> mri_watershed -atlas -s 114 164 45 -s 59 164 171 -s 66 198 171 -s 83 228
> 169 -s 81 228 158 -s 68 77 158 -s 68 108 65 -s 68 126 68 -s 68 141 71 -s
> 193 142 72 -s 193 150 76 -s 102 149 43 -s 114 159 43 -s 163 160 47 -s 87
> 120 47 -s 87 106 47 -s 88 96 47 -s 140 44 83 -s 58 100 83 -s 58 138 93 -s
> 183 63 128 -s 111 42 124 -s 51 118 124 -useSRAS -surf outer_skin_surface
> -brainsurf 059501
> /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/059501/mri/T1.mgz
>
> /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/059501/bem/watershed/ws
>
>
> Does anyone have any ideas how to fix this problem? This is my first time
> doing this, so feel free to point out anything obvious that I might have
> missed. Thank you.
>
> -- Santosh
>
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-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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