Great introduction: An introduction to diffusion tensor image analysis
Exploring intensities
Re different MD values, in theory nothing should matter in terms of raw intensities, as explained below. However, if there is a consistent pattern of low MD having high absolute dw/b0 values, then it might point to an issue.
Question - scaling?
I still cant work out why those mouse MD maps are so much lower in value.
I opened the tensors up to look at the RGB directions and they all look rehey are just not right - scaled?
I looked at the BOs and they are not different - so I ran the global timetrends on the raw files and got the values below - so the first 32 images are from a mouse that ends up with a LOW global MD and the second 32 images are from one with higher MD.
The 4 high ones are the B0 images
Answer - scaling is relative
From the intro to DTI paper, here is how the intensities are related. The image intensity (S~k~) is based on the b0 intensity (“S~0~) multiplied by the exponential. The exponential is smaller than 1 for non-zero b values. So, the key is how does the b0 relate to the dw. Across sesries, it’s hard to tell from global values if something is off.
