There are many non-invasive monitoring devices for use but many may not be entirely suitable, or too expensive or impractical. Which is the best? Transcranial doppler? EEG? Infra-red spectroscopy?
It really depends on what you are trying to monitor e.g. intracranial vessel occlusion/rechannelization, cortical perfussion/cerebral hemoglobin oxygen saturation. intracranial pressure, epileptic activity, etc.
There is a device for each marker so, what are you interested in?
If you need to validate changes in blood flow (effective occlusion of the middle cerebral artery, etc.), laser Doppler signal is the best way to go. Remember that in mice LDS can be easily recorded transcranially, while in rats it may be more of a problem due to much less transparent skull.
I recommend you to take a look at laser speckle applications (but these are more sophisticated):
EEG is a COMPLEMENTARY technique that can give you very valuable information about changes in neuronal activities in regions of interest but is not suitable for validating the extent of stroke or changes in blood flow. The same applies to infrared imaging (which to my best knowledge rarely if ever done transcranially).
Re-formulate you question and specify your experimental needs for a better advice.
Stroke is primarily a vascular catastrophe. Thus the vascular process must be monitored first of all . The brain dysfunction is secondary item during stroke. Therefore, monitoring of causal connection should be used as vascular innovation technology- http://angio-veritas.com/en/technologies/vascular-innovations/ and neural monitoring for feedback during the complex neurorehabilitation - http://angio-veritas.com/en/technologies/nejroreabilitatsiya-psyhonevrolohichnyh-hvoryh/
More information about my unique approach - http://lushchyk.org/en/prof.html