Hi all,
I am currently preprocessing 7T MP2RAGE anatomical data and have encountered two issues during brain extraction / skull stripping.
1. Incomplete dura removal
The dura is not removed cleanly in some subjects, especially in the occipital region. Residual dura remains in the brain mask and seems to affect later segmentation / reconstruction steps.
2. How to handle vessels
Large vessels are also difficult to deal with. In some cases they are retained in the mask, and I am not sure whether they should be removed as non-brain tissue or preserved during preprocessing. I would appreciate guidance on the recommended practice here, especially for 7T MP2RAGE.
So my main questions are:
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Is incomplete dura removal, particularly in the occipital lobe, a common problem in 7T MP2RAGE preprocessing?
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For vessels, should they ideally be removed during skull stripping, or is it acceptable to keep them at this stage?
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Are there recommended tools or pipelines that perform better for these two issues in 7T MP2RAGE data?
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Are there practical strategies for improving results, such as using INV1/INV2 images, T1 maps, additional masking, or morphological cleanup?
Any suggestions, recommended workflows, or references would be greatly appreciated.
Thank you.