Table 3.

Comparison between three approaches to obtain a template set for rats.

Paper	N/strain	MRI intensity corrections	Individual MRI registration previous average template	Template space	Probabilistic tissue segmentations	P & W atlas edition	Atlas-template registration	Neuroimaging applications
	MR system main field					N
Schweinhardt et al. (2003)	5/in vivo SD	Histogram equalization (not described)	Affine, based on minimizing the sum of the weighted distances between 49 landmarks pairs in the individual and atlas space	Paxinos and Watson	–	Second (Paxinos and Watson, 1989)	–	SPM spatial normalization. Right and left forepaw BOLD fMRI localization on the primary forelimb area of the somatosensory cortex (S1FL), visually evaluated (tested)
	4.7 T
Schwarz et al. (2006)	97/in vivo SD	Receiver coil correction and square root to reduce inter-variability and enhance tissue separation	PCA-based rigid to P & W atlas, matching brains and atlas outer surfaces	Arbitrary	Brain, brain parenchyma, and CSF	Fourth (Paxinos and Watson, 1998)	–	SPM spatial normalization. Pharmacological-induced perfusion MRI (phMRI) localization with volume of interest (VOI) evaluation of both localization and spatial extent (tested)
	4.7 T					468
Current	30/in vivo Wistar	Receiver coil correction, histogram equalization (1D linear registration) and, for segmentation, anisotropic filtering to enhance tissue separation	Highly non-linear, based on a multi-resolution, multi-grid scheme	Minimal deformation	Brain, gray matter, white matter, and CSF	Sixth and latest (Paxinos and Watson, 2007)	ATPS based on weighted landmarks	SPM spatial normalization, SPM tissue segmentation and atlasing in low resolution MRI. Right and left of both forepaw and hindpaw fMRI localization with quantitative ROI evaluation and volumetry (all tested). ROI–ROI DTI-based connectivity (future work) morphological connectivity (future work)
	7.0 T					96

Sprague-Dawley; P and W, Paxinos and Watson; ATPS, approximate thin plate splines.