A template-based automatic skull-stripping approach for mouse brain MR microscopy

Voluntary wheel running delays brain atrophy in aged mice

BACKGROUND:

Physical exercises have been shown to be a surprisingly effective strategy to take advantage of the brain’s natural capacity for plasticity, and prevent brain degeneration in mouse histological studies. In vivo magnetic resonance microscopy (MRM) provides highly resolved anatomical images and allows quantitative assessment of brain atrophy in the aged mouse model.

OBJECTIVE:

The aim of the present study was to investigate, through the effects of 10 weeks voluntary wheel running, the mouse’s brain atrophy.

METHODS:

Sixteen C57BL/6J mice, aged 21 months, were randomized to the exercise or sedentary group. Each mouse was scanned in a 7.0-T MRM scanner at two time points: 22 months old baseline and a follow-up three months later. Multi-atlas based brain segmentation approach was used to obtain volumes of 39 brain regions.

RESULTS:

The results showed that mice in the exercise group had less brain atrophy compared with the mice in the sedentary group.

CONCLUSIONS:

The results provide new insights into exercise induced brain plasticity in aged animals.

A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head

BACKGROUND

Magnetic resonance imaging (MRI) is a well-developed technique in neuroscience. Limitations in applying MRI to rodent models of neuropsychiatric disorders include the large number of animals required to achieve statistical significance, and the paucity of automation tools for the critical early step in processing, brain extraction, which prepares brain images for alignment and voxel-wise statistics.

NEW METHOD

This novel timesaving automation of template-based brain extraction ("skull-stripping") is capable of quickly and reliably extracting the brain from large numbers of whole head images in a single step. The method is simple to install and requires minimal user interaction.

RESULTS

This method is equally applicable to different types of MR images. Results were evaluated with Dice and Jacquard similarity indices and compared in 3D surface projections with other stripping approaches. Statistical comparisons demonstrate that individual variation of brain volumes are preserved.

COMPARISON WITH EXISTING METHODS

A downloadable software package not otherwise available for extraction of brains from whole head images is included here. This software tool increases speed, can be used with an atlas or a template from within the dataset, and produces masks that need little further refinement.

CONCLUSIONS

Our new automation can be applied to any MR dataset, since the starting point is a template mask generated specifically for that dataset. The method reliably and rapidly extracts brain images from whole head images, rendering them useable for subsequent analytical processing. This software tool will accelerate the exploitation of mouse models for the investigation of human brain disorders by MRI.