Can you send us the recon-all.log?
On Sep 3, 2009, at 4:29 AM, "Zheng Hui" zheng.hui@duke-nus.edu.sg wrote:
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
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
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