Assistance with Preprocessing Longitudinal T1w MRI Data in UKBB

Juhyeong Kang

I am conducting a study using longitudinal T1w MRI data from UKBB and encountered an issue. While the first imaging visit files seem fully preprocessed, the second imaging visit files (e.g., T1_orig_defaced.nii) appear only defaced without further preprocessing.

For consistency, I need to preprocess the second visit files in the same way as the first visit files. Unfortunately, I lack the background knowledge and am unsure how to proceed. Does UKBB provide a preprocessing pipeline or tools to handle this, or could you advise on the appropriate steps?

Your guidance would be greatly appreciated.

Comments

1 comment

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    Oliver G The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Juhyeong,

    The images available within field 20252 should have only the T1_orig_defaced.nii if the T1 was deemed of overly low quality for full processing through the UK Biobank brain imaging pipeline. Files that have been classified in this way should only have T1_orig_defaced.nii in the ‘unusable’ subfolder of the participants zip folder for 20252. These should be very few in number relative to the size of the cohort and second visit images shouldn't be more affected than the first imaging visit.

    Thanks,

    Ollie

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