Zhengchen Cai

@effigies Thanks a lot, you are the best !

> I have a pretty good computer, and am having a lot of problems using the Stan framework. 1st installation wasn't easy at all. But worse - even though I...

@jrdalenberg I had similar issues in this [post](https://neurostars.org/t/inaccurate-brain-mask-when-enabling-use-syn-sdc/22930). After rerunning fmriprep, it got better. Maybe this is not related to fmriprep versions, but rather the way ANTs extract the brain...

If it's BET for brain extraction, it is understandable since there might be a random initialization of the center of the brain, but fMRIprep is using ANTs which is templated-based...

Thanks for the clarification @effigies. Do you think it is possible to run a few brain extractions (e.g., 5) in the pipeline before proceeding and just select, by checking the...

Just to update this issue. I realized one can specify the brain extraction template in fmriprep. So I tried https://github.com/templateflow/tpl-MNI152NLin2009cAsym, ```--skull-strip-template MNI152NLin2009cAsym```. The brain extraction is still not good. I...