Fmriprep - wired brain extraction

Hi, there,

I got some weird brain mask from fmriprep. Could you please help me to see what is going on? Thx!

White is the mask from FSL bet, red is the mask from fmriprep:

If you look at the sag slices in your fmriprep output, you will notice how much brighter the parietal/occipital regions are compared to the inf. frontal regions. This requires ‘intensity normalization’ which IS a part of fmriprep, but occurs after brainmask creation. I’m not sure exactly why it failed, but if it is just one subject, you could try something like the linked code (you’ll need to download the whole set of scripts for it to work, or read through the code and just use the underyling FSL tool you need) to just prepare the T1 image first, then hand it back to fmriprep:

Thank you very much for you suggestion!

The original T1w volume doesn’t seem to have this brightness problem. So I guess it could be some side effect due to the incorrect brain extraction.

What I am doing now is to bypass the I use FSL bet to do brain extraction first and then run fmriprep without brain extraction. It works well, though I still have no idea why the doesn’t work for my dataset.

I believe this is another instance of this issue:

We are currently working on this