Hi Abisan
hmmm, can you tell why it is bright back there? Make sure it isn't nose
wrapping into the back of the head. Otherwise I would try some control
points
cheers
Bruce
On Wed, 25 Mar 2015, Abisan - wrote:
Hi FreeSurfer experts,
I have used "recon-all -all" on many T1w images and it has worked well. For
about 5% of volumes a lot of brain is removed during skullstripping. On
further inspection I have found that the T1.mgz for these individuals has
hyper-intensity in posterior parts of the brain. I've attached an example
image here. The raw images from the scanner look good, but do have a a large
signal intensity range and dynamic across the image.
Do you have suggestions for how to fix this? Is there an signal intensity
normalization step that can be tweaked? I've tried also changing the
-wsthresh in recon-all, which has helped some, but I think it would be
better to deal with the issue further upstream in the pipeline.
Thank you!
Abisan
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