Segmentation issue in fmriprep

I’m using fmriprep (version 1.5.4) and encountered some issues that appear to be related to the segmentation of anatomical images. As can be seen on the attached image, there are several voxels that are not identified properly. My intuition tells me it has something to do with the dimmed intensity at lower slices of the T1w images. Could someone provide me with some advice on how to deal this issue and achieve proper segmentation?

When running fmriprep, I’m using these two options:

Thank you