Dark images under functional and anatomical alignment section despite normal raw scans

Dear fMRIprep experts,

I am new to fMRIprep and noticed that dark images appeared under functional and anatomical alignment section for several participants despite normal raw scans (and normal maximum intensity values) based on visual inspection (a screenshot of two examples is provided below; lower one is more severe compared to the upper one). I was wondering what might be the potential causes of this and if it warrants exclusion of scans?

fmriprep version: 22.0.2 run on a HPC cluster

Command used: singularity run -B “{myproject}":"{myproject}” --cleanenv “{myproject}/fmriprep-22.0.2.simg" --skip-bids-validation "{myproject}/nina” “{myproject}/nina/nina_Processed" --mem_mb 30000 participant --participant-label "{SUBJECT}” --fs-license-file “${myproject}/license.txt” --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --use-aroma -w /tmp/

Type of SDC used: No SDC flag or fieldmap was used or included

Many thanks in advance for your assistance with this issue!

Hi @Yan_Tse, welcome to Neurostars!

To be able to help you, we would need more information: fmriprep version, command used, type of SDC used by fmriprep on your data etc… Could you create a new draft choosing the category “software support” and filling in all the relevant sections? Thank you!

Thank you so much for your prompt reply @jsein and so sorry for the lack of information.
I have now updated the post and changed the category, please let me know if any further information may be helpful.

Many thanks again!