Dear List,
I am consistently getting lower GM volume than WM volume when using Sienax. I have gone through the forums and tried various corrections including bias field correction and setting a -c option for bet (within Sienax) for better brain estimation, but the results are still the same. I have also run seinax with -d option and looked at intermediate images but do not see anything there either. What is slightly more disturbing is that with different values of -c option in bet, the volume estimated keeps changing quite a bit. What can I do about this... since I want to run this across 80 something subjects, I want to keep the parameters chosen consistent across subjects.
What would be some other things I could do...? If it helps I could upload a sample subject's image folder for any further pointers from you.
Thanks,
RN
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