Rat brain digital stereotaxic white matter atlas with fine tract delineation in Paxinos space and its automated applications in DTI data analysis.

PURPOSE To automatically analyze diffusion tensor images of the rat brain via both voxel-based and ROI-based approaches, we constructed a new white matter atlas of the rat brain with fine tracts delineation in the Paxinos and Watson space. MATERIALS AND METHODS Unlike in previous studies, we constructed a digital atlas image from the latest edition of the Paxinos and Watson. This atlas contains 111 carefully delineated white matter fibers. A white matter network of rat brain based on anatomy was constructed by locating the intersection of all these tracts and recording the nuclei on the pathway of each white matter tract. Moreover, a compatible rat brain template from DTI images was created and standardized into the atlas space. To evaluate the automated application of the atlas in DTI data analysis, a group of rats with right-side middle cerebral artery occlusion (MCAO) and those without were enrolled in this study. RESULTS The voxel-based analysis result shows that the brain region showing significant declines in signal in the MCAO rats was consistent with the occlusion position. CONCLUSION We constructed a stereotaxic white matter atlas of the rat brain with fine tract delineation and a compatible template for the data analysis of DTI images of the rat brain.

[1]  Tong Zhang,et al.  Dynamic metabolic changes after permanent cerebral ischemia in rats with/without post-stroke exercise: a positron emission tomography (PET) study , 2014, Neurological research.

[2]  Maria Giulia Preti,et al.  In vivo DTI tractography of the rat brain: an atlas of the main tracts in Paxinos space with histological comparison. , 2015, Magnetic resonance imaging.

[3]  Arthur W. Toga,et al.  Human brain white matter atlas: Identification and assignment of common anatomical structures in superficial white matter , 2008, NeuroImage.

[4]  Dominique Hasboun,et al.  Anatomically constrained region deformation for the automated segmentation of the hippocampus and the amygdala: Method and validation on controls and patients with Alzheimer’s disease , 2007, NeuroImage.

[5]  Stamatios N. Sotiropoulos,et al.  A probabilistic atlas of the cerebellar white matter , 2016, NeuroImage.

[6]  Yundi Shi,et al.  A diffusion tensor MRI atlas of the postmortem rhesus macaque brain , 2015, NeuroImage.

[7]  P. Weinstein,et al.  Reversible middle cerebral artery occlusion without craniectomy in rats. , 1989, Stroke.

[8]  Lan Lin,et al.  Construction of mouse brain MRI templates using SPM 99 , 2003 .

[9]  Trygve B. Leergaard,et al.  Waxholm Space atlas of the Sprague Dawley rat brain , 2014, NeuroImage.

[10]  L. Swanson.  The Rat Brain in Stereotaxic Coordinates, George Paxinos, Charles Watson (Eds.). Academic Press, San Diego, CA (1982), vii + 153, $35.00, ISBN: 0 125 47620 5 , 1984 .

[11]  I. Oguz,et al.  3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain , 2013, PloS one.

[12]  Trygve B. Leergaard,et al.  Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging , 2015, NeuroImage.

[13]  Peter Zhilkin,et al.  Affine registration: a comparison of several programs. , 2004, Magnetic resonance imaging.

[14]  Murali Murugavel,et al.  Automatic cropping of MRI rat brain volumes using pulse coupled neural networks , 2009, NeuroImage.

[15]  Rafael C. González,et al.  Digital image processing using MATLAB , 2006 .

[16]  G. Paxinos,et al.  The Rat Brain in Stereotaxic Coordinates , 1983 .

[17]  Habib Zaidi,et al.  Automated analysis of small animal PET studies through deformable registration to an atlas , 2012, European Journal of Nuclear Medicine and Molecular Imaging.

[18]  Roustem Khazipov,et al.  Atlas of the Postnatal Rat Brain in Stereotaxic Coordinates , 2015, Front. Neuroanat..

[19]  Charles Watson,et al.  MRI/DTI Atlas of the Rat Brain , 2015 .

[20]  Andrea Bergmann,et al.  Statistical Parametric Mapping The Analysis Of Functional Brain Images , 2016 .

[21]  V. Girish,et al.  Affordable image analysis using NIH Image/ImageJ. , 2004, Indian journal of cancer.

[22]  Ewart R. Carson,et al.  Modelling and control in biomedical systems , 2011, Comput. Methods Programs Biomed..

[23]  Kurt Wisner,et al.  Ratat1: A Digital Rat Brain Stereotaxic Atlas Derived from High-Resolution MRI Images Scanned in Three Dimensions , 2016, Front. Syst. Neurosci..

[24]  Zhengyi Yang,et al.  MRI-guided volume reconstruction of mouse brain from histological sections , 2012, Journal of Neuroscience Methods.

[25]  Karl J. Friston,et al.  Statistical parametric mapping , 2013 .

[26]  C H Rabb,et al.  Nylon monofilament for intraluminal middle cerebral artery occlusion in rats. , 1996, Stroke.

[27]  Yi Jiang,et al.  Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain , 2011, NeuroImage.

[28]  Alexander Hammers,et al.  Evaluation of atlas-based segmentation of hippocampi in healthy humans. , 2009, Magnetic resonance imaging.

[29]  Binbin Nie,et al.  A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel‐wise analysis , 2013, Human brain mapping.

[30]  G. Allan Johnson,et al.  A multidimensional magnetic resonance histology atlas of the Wistar rat brain , 2012, NeuroImage.

[31]  M. Raichle,et al.  Rat brains also have a default mode network , 2012, Proceedings of the National Academy of Sciences.

[32]  N. Logothetis,et al.  A combined MRI and histology atlas of the rhesus monkey brain in stereotaxic coordinates , 2007 .

[33]  Arthur W. Toga,et al.  Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template , 2008, NeuroImage.

[34]  K Minematsu,et al.  Nylon monofilament for intraluminal middle cerebral artery occlusion in rats. , 1995, Stroke.