Hi Niels,

This looks like what would happen to the aseg if it was run on a subject who was missing a cerebellum. Did you run the aseg before you manually fixed the cerebellum and not re-run it? If so, the aseg needs to be rerun (in fact, all of -autorecon2 does).

Another thought is, how did you manually edit to fix the missing cerebellum? Did you use command line procedures, like increasing the preflooding height or using the option -wsatlas? Or did you do it by hand with the "edit voxels" tool in tkmedit? If you've done it by hand, were you on the appropriate volume (brainmask.mgz) and did you do it for every slice that there was missing cerebellum?

My recommendation for fixing a completely missing cerebellum is always to use the command line. Increasing the preflooding height (or using the atlas flag) should work everytime: recon-all -skullstrip -wsthresh 35 -clean-bm -s <subject> recon-all -skullstrip -wsatlas -clean-bm -s <subject>

Jenni

On Fri, 5 Jan 2007, Niels Bergsland wrote:

Hi list, After completing autorecon1, I found the cerebellum missing and I manually editted for this case. But I found after autorecon2, the cerebellum were not filled with appropriate color at all. I have uploaded a picture to my webspace. Please see: http://www.lucidthoughts.org/download/color_failure.png

I can also upload the dicoms to the drop box if this would help. Thanks!

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