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PyFaceWipe: a new defacing tool for almost any MRI contrast

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Magnetic Resonance Materials in Physics, Biology and Medicine Aims and scope Submit manuscript

Abstract

Rationale and objectives

Defacing research MRI brain scans is often a mandatory step. With current defacing software, there are issues with Windows compatibility and researcher doubt regarding the adequacy of preservation of brain voxels in non-T1w scans. To address this, we developed PyFaceWipe, a multiplatform software for multiple MRI contrasts, which was evaluated based on its anonymisation ability and effect on downstream processing.

Materials and methods

Multiple MRI brain scan contrasts from the OASIS-3 dataset were defaced with PyFaceWipe and PyDeface and manually assessed for brain voxel preservation, remnant facial features and effect on automated face detection. Original and PyFaceWipe-defaced data from locally acquired T1w structural scans underwent volumetry with FastSurfer and brain atlas generation with ANTS.

Results

214 MRI scans of several contrasts from OASIS-3 were successfully processed with both PyFaceWipe and PyDeface. PyFaceWipe maintained complete brain voxel preservation in all tested contrasts except ASL (45%) and DWI (90%), and PyDeface in all tested contrasts except ASL (95%), BOLD (25%), DWI (40%) and T2* (25%). Manual review of PyFaceWipe showed no failures of facial feature removal. Pinna removal was less successful (6% of T1 scans showed residual complete pinna). PyDeface achieved 5.1% failure rate. Automated detection found no faces in PyFaceWipe-defaced scans, 19 faces in PyDeface scans compared with 78 from the 224 original scans. Brain atlas generation showed no significant difference between atlases created from original and defaced data in both young adulthood and late elderly cohorts. Structural volumetry dice scores were ≥ 0.98 for all structures except for grey matter which had 0.93. PyFaceWipe output was identical across the tested operating systems.

Conclusion

PyFaceWipe is a promising multiplatform defacing tool, demonstrating excellent brain voxel preservation and competitive defacing in multiple MRI contrasts, performing favourably against PyDeface. ASL, BOLD, DWI and T2* scans did not produce recognisable 3D renders and hence should not require defacing. Structural volumetry dice scores (≥ 0.98) were higher than previously published FreeSurfer results, except for grey matter which were comparable. The effect is measurable and care should be exercised during studies. ANTS atlas creation showed no significant effect from PyFaceWipe defacing.

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Data availability

The source data used in this evaluation was from a combination of the OASIS3 database and local clinical scans which we are unable to share. I am happy to share the scripts used to automate generation of the renders and facial recognition. Volumetry data from FastSurfer can be made available on request.

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Acknowledgements

Data were provided in part by OASIS-3 [Longitudinal Multimodal Neuroimaging: Principal Investigators: T. Benzinger, D. Marcus, J. Morris; NIH P30 AG066444, P50 AG00561, P30 NS09857781, P01 AG026276, P01 AG003991, R01 AG043434, UL1 TR000448, R01 EB009352. AV-45 doses were provided by Avid Radiopharmaceuticals, a wholly owned subsidiary of Eli Lilly].

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Authors and Affiliations

  1. Department of Radiology, Sengkang General Hospital, Singhealth, 110 Sengkang E Way, Singapore, 544886, Singapore

    Stanislaw Mitew, Chi Long Ho & Oliver James Nickalls

  2. Clinical Data Analytics & Radiomics Group, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 30 Biopolis St, Matrix, Singapore, 138671, Singapore

    Ling Yun Yeow & Prakash K. N. Bhanu

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  1. Stanislaw Mitew
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Correspondence to Oliver James Nickalls.

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Mitew, S., Yeow, L.Y., Ho, C.L. et al. PyFaceWipe: a new defacing tool for almost any MRI contrast. Magn Reson Mater Phy (2024). https://doi.org/10.1007/s10334-024-01170-x

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