Development of new population-averaged standard templates for spatial normalization and segmentation of MR images for postnatal piglet brains

An In vivo Multi-Modal Structural Template for Neonatal Piglets Using High Angular Resolution and Population-Based Whole-Brain Tractography

“…Compared to the existing two piglet T1 templates, this T1 template includes higher GM/WM contrast retaining more detailed information than the one from Conrad et al (2014) and is more comprehensive, including both the optic chiasm and olfactory bulb, relative to the one generated by Gan et al (2014) .…”

“…A standard coordinate system is important for brain research, where reported brain locations could be easily compared across studies and imaging modalities. In order to maintain consistency with other templates ( Felix et al, 1999 ; Watanabe et al, 2001 ; Saikali et al, 2010 ; Conrad et al, 2014 ; Gan et al, 2014 ), we set the same origin at the anterior limit of the posterior commissure in the midsagittal plane. This eases the comparison of results from studies with different templates.…”

“…The template was then reoriented along a line connecting the centers of the anterior and posterior commissure (y-axis). The origin was set to be the anterior limit of the posterior commissure in the midsagittal plane, consistent with published pig templates ( Felix et al, 1999 ; Watanabe et al, 2001 ; Saikali et al, 2010 ; Conrad et al, 2014 ; Gan et al, 2014 ). The FMRIB’s Automated Segmentation Tool (FAST) of FSL (Analysis Group, FMRIB, Oxford, UK) 2 was applied to segment the individual brains into GM, WM, and CSF.…”

“…Still, this template lacks adequate sulcal and gyral information because linear registration was performed to generate the template and non-linear deformation fields were only applied to compensate for template shape or morphology. Gan et al (2014) generated a T1 template based on a group of neonatal piglets (38 days old, Suscrofa × Landrace × Large White F1). The Gan template shows improved gray matter/white matter (GM/WM) contrast, however, important anatomical areas such as the optic chiasm and bulbus olfactorius needed to be removed to allow for better positional accuracy, limiting the usability of this template.…”

In vivo Population Averaged Stereotaxic T2w MRI Brain Template for the Adult Yucatan Micropig

“…Numerous such templates have been developed over the years for this purpose in humans (Fonov et al, 2009), non-human primate species (Quallo et al, 2010;Frey et al, 2011), dogs (Nitzsche et al, 2019), cats (Stolzberg et al, 2017), sheep (Nitzsche et al, 2015), and rodents (Bai et al, 2012;Papp et al, 2014). Several MRI-based brain atlases have been created for the pig model (Watanabe et al, 2001;Saikali et al, 2010;Conrad et al, 2014;Gan et al, 2014;Zhong et al, 2016), although with important limitations for the abovementioned use case. Most previous templates have been created in neonatal piglets (3-6 weeks old) for use as a neurodevelopmental model (Conrad et al, 2014;Gan et al, 2014;Zhong et al, 2016), with significant morphological differences to the sexuallymature pig brain (Conrad et al, 2012;Zhong et al, 2016).…”