A technique for the deidentification of structural brain MR images

Abstract

Due to the increasing need for subject privacy, the ability to deidentify structural MR images so that they do not provide full facial detail is desirable. A program was developed that uses models of nonbrain structures for removing potentially identifying facial features. When a novel image is presented, the optimal linear transform is computed for the input volume (Fischl et al. [2002]: Neuron 33:341-355; Fischl et al. [2004]: Neuroimage 23 (Suppl 1):S69-S84). A brain mask is constructed by forming the union of all voxels with nonzero probability of being brain and then morphologically dilated. All voxels outside the mask with a nonzero probability of being a facial feature are set to 0. The algorithm was applied to 342 datasets that included two different T1-weighted pulse sequences and four different diagnoses (depressed, Alzheimer's, and elderly and young control groups). Visual inspection showed none had brain tissue removed. In a detailed analysis of the impact of defacing on skull-stripping, 16 datasets were bias corrected with N3 (Sled et al. [1998]: IEEE Trans Med Imaging 17:87-97), defaced, and then skull-stripped using either a hybrid watershed algorithm (Ségonne et al. [2004]: Neuroimage 22:1060-1075, in FreeSurfer) or Brain Surface Extractor (Sandor and Leahy [1997]: IEEE Trans Med Imaging 16:41-54; Shattuck et al. [2001]: Neuroimage 13:856-876); defacing did not appreciably influence the outcome of skull-stripping. Results suggested that the automatic defacing algorithm is robust, efficiently removes nonbrain tissue, and does not unduly influence the outcome of the processing methods utilized; in some cases, skull-stripping was improved. Analyses support this algorithm as a viable method to allow data sharing with minimal data alteration within large-scale multisite projects.

Figure 1

An example of a 3‐D reconstruction of a T1‐weighted dataset (a) before and (b) after application of the defacing algorithm. The defacing algorithm removed identifying facial features while preserving brain tissue for future analyses.

Figure 2

A sagittal slice from a defaced dataset illustrating how nonbrain voxels in the face region are set to a fill value of zero.

Figure 3

Standard location of the manually stripped slices as demonstrated on a coronal image.

Figure 4

Examples of successful application of the defacing algorithm. Top row: elderly control subject (left) and Alzheimer's patient (right); bottom row: young normal control subject (left) and unipolar depressed patient (right).

Figure 5

Mean (standard error bars) for (a) Jaccard Similarity Coefficient (JSC) and (b) Hausdorff Distance for Diagnosis by Method relative to the manually stripped slices for Anatomist 1 (Six Slice analysis). DEF: defaced; HWA: Hybrid Watershed.