Computational protocol: A high-resolution cardiovascular magnetic resonance diffusion tensor map from ex-vivo C57BL/6 murine hearts

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Protocol publication

[…] Estimation-Registrations of Diffusion Tensors: The diffusion weighted MR images were imported into the Diffusion Toolkit (Massachusetts General Hospital, Boston, MA, USA; along with the corresponding gradient table and b–value, and the diffusion tensors for each dataset were calculated (Figure ). All diffusion datasets were co-registered with the corresponding b0 images (Figure ). Registration was performed using the Advanced Normalization Tools (ANTs) []. The geodesic mean, group-wise methodology [,,,,] was adopted. According to this methodology, a source heart image set was chosen (template) from the population of imaged (target) datasets mapped to the template heart [,,,,]. This process defined a new template heart, and the methodology was then iteratively repeated until an average geometry was obtained that resided within the center of all target geometries (Figure , ). Specifically, Large Diffeomorphic Metric Mapping (LDDMM) [] with Geodesic Symmetric Normalization (SyN) transformation [] was applied to register each target dataset to the current template dataset (Figure ).Figure 1Figure 2Figure 3Mutual information was defined as the similarity metric of the registered b0 images. The quality of the process was assessed using the union overlap measure (Jaccard coefficient) [], by summing the myocardial voxels in the target image that matched myocardial voxels in the template image, and dividing by the total number of myocardial voxels (Figure ). The resulting transformation matrices and deformation fields obtained from the b0 image registration were subsequently used to register datasets to the reference template of the heart geometry, and to reorient the diffusion tensors using the Preservation of the Principle Direction (PPD) methodology []. […]

Pipeline specifications

Software tools DTK, TrackVis
Application Diffusion magnetic resonance imaging analysis
Organisms Mus musculus, Homo sapiens, Canis lupus familiaris