Animations and captions relating to the registration of healthy volunteer free-breathing dynamic lung OE-MRI data. Supplementary thesis material.

<table><tr><td><p dir="ltr">Animations to illustrate the performance of different registration software applied to dynamic free-breathing lung oxygen-enhanced MRI (OE-MRI) data. NiftyReg and ANTs registration software were implemented.</p><p dir="ltr">See the <i>Animations Captions</i> <i>PDF document</i> for detailed descriptions of the registered image series.</p><p dir="ltr"><br></p></td></tr></table><p dir="ltr"><b><u>NiftyReg registration:</u></b></p><p dir="ltr">M. Modat et al. “Fast free-form deformation using graphics processing units". In: <i>Computer Methods and Programs in Biomedicine</i> 98.3 (2010), pp. 278-284. ISSN: 01692607. DOI: 10.1016/j.cmpb.2009.09.002.</p><p dir="ltr">M. Modat et al. “Parametric non-rigid registration using a stationary velocity field". In: <i>2012 IEEE Workshop on Mathematical Methods in Biomedical Image Analysis</i>. 2012, pp. 145-150. DOI: 10.1109/MMBIA.2012.6164745.</p><p dir="ltr"><b>Details of the NiftyReg registration implementation:</b></p><table><tr><td><p dir="ltr">Multi-resolution levels</p></td><td><p>3</p></td></tr><tr><td><p dir="ltr">Control point grid spacing</p></td><td><p dir="ltr">3 voxels, 14.1 mm final spacing</p></td></tr><tr><td><p dir="ltr">Similarity metric</p></td><td><p dir="ltr">Locally normalised cross-correlation</p></td></tr><tr><td><p dir="ltr">Penalty terms and weights</p></td><td><p dir="ltr">Bending energy, 5 x10^-3</p><p dir="ltr">Linear elastic energy, 1 x 10^-2</p></td></tr><tr><td><p dir="ltr">Transformation parameterisation</p></td><td><p dir="ltr">Stationary velocity field</p></td></tr><tr><td><p dir="ltr">Maximum number of iterations per resolution level</p></td><td><p>600, 300, 150</p></td></tr></table><table><tr><td><p><br></p><p><br></p><p dir="ltr"><b><u>ANTs registration:</u></b></p><p dir="ltr">B. B. Avants et al. “Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain." In: <i>Medical image analysis</i> 12.1 (2008), pp. 26-41. ISSN: 1361-8423 (Electronic). DOI: 10.1016/j.media.2007.06.004.</p><p dir="ltr">B. B. Avants et al. “A reproducible evaluation of ANTs similarity metric performance in brain image registration". In: <i>NeuroImage</i> 54.3 (2011), pp. 2033-2044. ISSN: 1053-8119. DOI: https://doi.org/10.1016/j.neuroimage.2010.09.025.</p><p dir="ltr">N. Tustison and B. Avants. “Explicit B-spline regularization in diffeomorphic image registration". In: <i>Frontiers in Neuroinformatics</i> 7 (2013). DOI: 10.3389/fninf.2013.00039.</p><p dir="ltr">B. B. Avants et al. “The Insight ToolKit image registration frame-work". In: <i>Frontiers in Neuroinformatics</i> 8 (2014). DOI: 10.3389/fninf.2014.00044.</p><p dir="ltr"><b>Details of the ANTs registration implementation:</b></p><table><tr><td><p dir="ltr">Multi-resolution levels</p></td><td><p>4</p></td></tr><tr><td><p dir="ltr">Smoothing parameters</p></td><td><p dir="ltr">2 x 2 x 0 x 0 mm</p></td></tr><tr><td><p dir="ltr">Gradient step</p></td><td><p>0.1</p></td></tr><tr><td><p dir="ltr">Update field variance in voxel space</p></td><td><p>3</p></td></tr><tr><td><p dir="ltr">Total field variance in voxel space</p></td><td><p>0</p></td></tr><tr><td><p dir="ltr">Update field knot spacing</p></td><td><p dir="ltr">26 mm</p></td></tr><tr><td><p dir="ltr">Similarity metric</p></td><td><p dir="ltr">Cross-correlation</p></td></tr><tr><td><p dir="ltr">Metric radius</p></td><td><p>2</p></td></tr><tr><td><p dir="ltr">Metric weight</p></td><td><p>1</p></td></tr><tr><td><p dir="ltr">Convergence parameter</p></td><td><p dir="ltr">500 x 200 x 100 x 50</p></td></tr></table><p><br></p><p><br></p></td></tr></table><p></p>