Empowering Data Sharing in Neuroscience: A Deep Learning Deidentification Method for Pediatric Brain MRIs
Bibliographic record
Abstract
ABSTRACT BACKGROUND AND PURPOSE: Privacy concerns, such as identifiable facial features within brain scans, have hindered the availability of pediatric neuroimaging datasets for research. Consequently, pediatric neuroscience research lags adult counterparts, particularly in rare disease and under-represented populations. The removal of face regions (image defacing) can mitigate this, however existing defacing tools often fail with pediatric cases and diverse image types, leaving a critical gap in data accessibility. Given recent NIH data sharing mandates, novel solutions are a critical need. MATERIALS AND METHODS: To develop an AI-powered tool for automatic defacing of pediatric brain MRIs, deep learning methodologies (nnU-Net) were employed using a large, diverse multi-institutional dataset of clinical radiology images. This included multi-parametric MRIs (T1w, T1w-contrast enhanced, T2w, T2w-FLAIR) with 976 total images from 208 brain tumor patients (Children’s Brain Tumor Network, CBTN) and 36 clinical control patients (Scans with Limited Imaging Pathology, SLIP) ranging in age from 7 days to 21 years old. RESULTS: Face and ear removal accuracy for withheld testing data was the primary measure of model performance. Potential influences of defacing on downstream research usage were evaluated with standard image processing and AI-based pipelines. Group-level statistical trends were compared between original (non-defaced) and defaced images. Across image types, the model had high accuracy for removing face regions (mean accuracy, 98%; N=98 subjects/392 images), with lower performance for removal of ears (73%). Analysis of global and regional brain measures (SLIP cohort) showed minimal differences between original and defaced outputs (mean rS=0.93, all p < 0.0001). AI-generated whole brain and tumor volumes (CBTN cohort) and temporalis muscle metrics (volume, cross-sectional area, centile scores; SLIP cohort) were not significantly affected by image defacing (all rS>0.9, p<0.0001). CONCLUSIONS: The defacing model demonstrates efficacy in removing facial regions across multiple MRI types and exhibits minimal impact on downstream research usage. A software package with the trained model is freely provided for wider use and further development (pediatric-auto-defacer; https://github.com/d3b-center/pediatric-auto-defacer-public). By offering a solution tailored to pediatric cases and multiple MRI sequences, this defacing tool will expedite research efforts and promote broader adoption of data sharing practices within the neuroscience community. ABBREVIATIONS: AI = artificial intelligence; CBTN = Children’s Brain Tumor Network; CSA = cross-sectional area; SLIP = Scans with Limited Imaging Pathology; TMT = temporalis muscle thickness; NIH = National Institute of Health; LH = left hemisphere; RH = right hemisphere.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.005 | 0.011 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.004 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".