MRI phase images are increasingly used, for example for Susceptibility Mapping, and distortion correction in functional and diffusion MRI. However, measured phase images contain wraps, because the phase is defined only between 0 and 2π. PRELUDE is the current gold-standard method for robust, 3D, spatial phase unwrapping, but its computation time can become very long (e.g. 10 hours), especially at high field and outside the brain. Here, we developed a new method, SEGUE, that produced similar results to PRELUDE in multi-echo brain and head-and-neck images, successfully unwrapped some regions where PRELUDE failed and was between 1.6 and 83 times faster.
In PRELUDE13-14, the phase map is partitioned into connected regions by dividing the [0, 2π] interval into 6 smaller, equal intervals. These regions are then unwrapped and merged by adding integer multiples of 2π to one of two neighbouring regions assuming spatial smoothness of the phase. This process continues until all the regions are merged. Tc increases with the number of initial regions. In high-resolution images, a single region can erroneously contain a wrap if it consists of areas with phase difference > 2π connected by a few noisy voxels. To avoid this, PRELUDE limits the initial regions to be 2D for high-resolution images (voxel size < 1 mm). This increases the number of initial regions and, consequently, Tc.
In SEGUE, we first divide the [0, 2π] interval into 6 intervals (similarly to PRELUDE) to determine the initial regions. Instead of restricting the regions to be 2D, small bridges of a few voxels between larger areas are removed before partitioning to avoid wraps within the 3D regions (Figure 1). The region with the largest border (Rm) is then selected and all the adjacent regions (Ra) that meet the following criteria are simultaneously unwrapped and merged with Rm: 1. The border between Rm and Ra is greater than P = 30% of the entire border of Ra. 2. A substantial proportion of neighbouring voxel pairs in Rm and Ra agree on the phase difference between Rm and Ra. When no more regions can be merged with Rm, a new Rm is selected and this process is repeated until at least 70% of the tissue mask is unwrapped. The entire merging process is repeated with P = 10% and P = 0% respectively.
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