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1Department of Radiology, University of Minnesota, Minneapolis, USA, 2Institute for Mathematics and its Applications, University of Minnesota, Minneapolis, USA, 3Department of Neurology, University of Minnesota, Minneapolis, USA |
| Modeling & Analysis Abstract |
| Labelling an MRI brain volume is a demanding task
-- tracking sulci and gyri through a 3D volume is non-trivial. Volume labelling
is voxel-based and typically performed using orthogonal slices through the
volume. When a cortical surface is extracted from an MRI volume it acquires
its labels from the voxel labelling and, ideally, the surface labels are
reconciled with the volume labels. In practice, flaws in a volume labelling
can become apparent when they are transferred to an extracted cortical surface
(Figure 1, left). Although much of the cortical surface is buried, examination of the cortex is useful for tracking gyri and defining anatomical landmarks. A surface represented by a triangulated mesh with the appropriate topology can be remapped to a sphere or "inflated" brain to reveal buried cortex [1,2,3]. ParcelMan permits a user to paint labels on linked representations of the cortical surface -- one folded ("wrinkled") and one conformally mapped to a sphere (Figure 1, right). This permits the user to view buried cortex and define contiguous patches. Embedding a surface labelling into an MRI volume can guide creation or correction of a voxel-based labelling but leaves the majority of cortical voxels unlabelled. To address this problem we have developed a tool (Pigment) for allowing surface paint to "seep" into cortical grey matter. The seepage is governed by directionality and tissue-weighting rules, and a contiguous patch of surface is expected to contribute to subjacent cortex. In a pilot experiment the cortical surface of a left hemisphere was extracted from a T1 MRI volume; anatomical labels for that volume were provided by N. Kabani, University of Toronto. Gyral labels for the volume were grouped into lobe labels (Figure 2; left) and used to provide labels for the cortical surface. Grey-white tissue segmentation [4] of the MRI volume identified the voxels where seepage was permitted. Surface labels were corrected to form contiguous patches (Figure 2; center) and allowed to seep into the cortex (Figure 2; right). Although not every sulcus was accurately represented in our surface mesh, the labels that were propagated into the MRI volume from the mesh reproduced the expert labels in 88% of grey-matter voxels. Of the mismatched labels, some resulted from problems in the expert labelling -- as evidenced by isolated white voxels (Figure 2; left). We hypothesize that using a labelled cortical surface to initialize volume labelling can significantly reduce the effort of manual parcellation, and that a combination of surface- and volume-based tools will permit volume and surface labels to be reconciled in a principled manner. 1. Hurdal M, et al.(1999). Lec. Notes in Comp. Sci. Springer-Verlag, Berlin. Vol 1679; 279-286. 2. Fischl B, et al.(1999). NeuroImage 9(2):195-207. 3. Ju L, et al. (2004). NeuroImage 19:S864. 4. Collins D,et al. (1995). Human Brain Mapping, 3(3):190-208. This work was supported in part by NIH grant EB02013. |
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