Dear Bruce,

In the attached image at the ventricle area, you can see the pial and white surfaces go into the ventricle, following the white/CSF boundary rather than going through the medial separation. And by looking at the wm.mgz, I can see the ventricles were not filled by the program although the ventricles were labelled correctly in aseg.mgz. Hope I describe the problem clearer this time. I have attached the image again.

Thanks,
Zheng Hui

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Hi Zheng,

sorry, I don't see what you mean in the image. If you want to upload a
dataset that has this problem I'll take a look.

cheers,
Bruce
On Wed, 2 Sep 2009, Hui
Zheng wrote:

> Hi freesurfer,
>
> We are reprocessing our data from FS version 3.05 with the latest 4.50. We
> found there are about 20% of the subjects have problem at the ventricle as
> shown in the attached image. I have tried the method suggested by Doug to
> remove the wm.mgz and rerun from autorecon2-cp. However, for two subjects I
> have tried, the method did not help. It will be tedious to manually fill in
> all the ventricles in wm.mgz. Any other work around?
>
> Thanks,
> Zheng Hui
>
>