I found that one of my fmriprep output might have some signal loss in functional images, during the function-structural alignment outputs. Below is the screenshot:
When I overlay the grey matter mask and the preprocessed functional images in fsleyes, it looks like this:
I can see indeed that there are some signal loss in the grey matter area. I wonder if this is something I need to fix in my preprocessing pipeline, or it’s just a data quality issue. Any suggestions and related experience would be helpful!