Problematic alignment of T1w from two subjects


I run fmriprep using this command:

sudo /home/…/.local/bin/fmriprep-docker …/Data/BIDS …/Data/BIDS/derivatives participant --participant-label 001 --fs-license-file /usr/local/freesurfer/license.txt

There were no errors reported in the .html file.
Then I opened the T1w files (sub-002_desc-preproc_T1w.nii.gz) for 2 subjects to check the alignment and it appears that it’s not as expected. You may check the attached screenshot from itksnap.
Can anyone hint on what may have gone wrong or on how to retry for a better result?

Thank you for your time!

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