Hi all,
I am working with mouse brain T2 MRI data and want to analyze volumetric differences in specific brain regions, including the hippocampus, lateral ventricles (LV), cortex, and corpus callosum (CC), between normal and Alzheimer's disease (AD) mouse models. As I am new to this type of analysis and interpretation, I would greatly appreciate your guidance on the following:
Dear Dr. Sharma,
As you are new to this area unless you are willing to setup some automated measurement software, test it and validate it, you will doing these measurements manually by tracing regions-of-interest (ROIs) by eye on your images.
For this you will need a program that reads your image format and allows making these measurements. A freely available one is FIJI at https://fiji.sc/. It is based off the NIH ImageJ software but with a lot of added functions. Second you will need a mouse brain atlas to guide you on the neuroanatomy of the MRI images based on the location the images were taken from. As you are using T2 weighted images you will easily identify the ventricles as they will be hyperintense. Depending on the MR acquisition parameters (TE) you may have good grey/white matter delineation also. From here you will have most of the visual cues to identify the structures from the atlas.
Go check out FIJI and it includes a MRI data set that can be practiced on. Try to load your mouse images and see if you can trace out the structure with the ROI tool. You can test your reproducibility error by doing an ROI trace on a structure say 5 different times. This will give you your standard error for your method of measurement. You can then use that to determine the differences between your experimental cohort. Of course for completeness you will want to perform this standard of error test on the extrema of your cohort and the median to make certain your don't have a systematic error from size differences.
That should get you started. Good Luck.
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