I know that many labs develop custom MATLAB scripts for using in the laboratory. I am wondering if anyone knows of any that are freely available for download or that they would be willing to share for use with neuroanatomy (e.g., tract-tracing etc.)?
if you use the SPM software,
http://www.fil.ion.ucl.ac.uk/spm/software/
you can convert your images to the NIfTI file format, and scale the 3 spatial dimensions of the rat/mouse anatomy with a factor of 10. (e.g a voxel size of 100 micrometer becomes 1mm). This helps for visualizing the data and gives you full functionality of all available tools.
For actions like segmentation and normalization of MRI images there is an atlas for rat anatomy (Sprague Dawley) available at the Karolinska that may come in handy: http://expmr.ki.se/research/ratatlas.jsp
For other weightings, or imaging techniques, you can generate your own atlas, similar to http://www.ncbi.nlm.nih.gov/pubmed/21749925
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