Hi Santosh,<br><br>What specifically is the problem with the outer skin?<br><br>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 <b>tkmedit <subject> T1.mgz</b>.<br>
<br>Best,<br>Steve Politzer-Ahles<br><br><div class="gmail_quote">On Mon, Apr 2, 2012 at 11:15 AM, <span dir="ltr"><<a href="mailto:santosh@nmr.mgh.harvard.edu">santosh@nmr.mgh.harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I have a MRI subject, where once we performed reconstruction, the<br>
brain came out fine, but the outer skin was not properly<br>
reconstructed. I tried using mri_watershed to manually add control<br>
points in order to try to rectify this problem, with no luck. Here is<br>
the command.<br>
<br>
<br>
mri_watershed -atlas -s 114 164 45 -s 59 164 171 -s 66 198 171 -s 83 228<br>
169 -s 81 228 158 -s 68 77 158 -s 68 108 65 -s 68 126 68 -s 68 141 71 -s<br>
193 142 72 -s 193 150 76 -s 102 149 43 -s 114 159 43 -s 163 160 47 -s 87<br>
120 47 -s 87 106 47 -s 88 96 47 -s 140 44 83 -s 58 100 83 -s 58 138 93 -s<br>
183 63 128 -s 111 42 124 -s 51 118 124 -useSRAS -surf outer_skin_surface<br>
-brainsurf 059501<br>
/autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/059501/mri/T1.mgz<br>
/autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/059501/bem/watershed/ws<br>
<br>
<br>
Does anyone have any ideas how to fix this problem? This is my first time<br>
doing this, so feel free to point out anything obvious that I might have<br>
missed. Thank you.<br>
<br>
-- Santosh<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Stephen Politzer-Ahles<br>University of Kansas<br>Linguistics Department<br><a href="http://www.linguistics.ku.edu/">http://www.linguistics.ku.edu/</a><br>