The testData folder contains an input/output example for a T1-weighted rat brain image. 

You can replicate these results with:
RATS_MM rat_t1.nrrd rat_t1_mm.nii.gz -t 500 -v 1650
and
RATS_LOGISMOS rat_t1.nrrd rat_t1_mm.nii.gz rat_t1_logismos.vtp --alpha 5

Details regarding input/output can be obtained by typing:
RATS_MM --help
and
RATS_LOGISMOS --help

For the interpretation of the parameters, as well as for further details regarding the algorithm, please refer to:
Oguz, Zhang, Rumple, Sonka, RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI. Journal of neuroscience methods (2014) vol. 221 pp. 175 - 182

Please contact ipek-oguz@uiowa.edu for any questions and feedback.
