Dear colleagues,
Much more often (to my impression) than in human neuroimaging, preclinical MRI (of rodents) is performed with anisotropic voxels, where slice thickness is commonly multiple times larger than in-plane resolution.
I am assuming there has to be more technical reasons for it than just historical similarity to microscopy/histology, but have not yet been able to pinpoint the underlying physical principle. (Maybe this is related to gradient strength or the use of coils with less channels?) Your expertise and any references regarding this topic is highly welcomed.
Thank you very much in advance and happy holidays!
Hi Peter,
You make an astute observation. The short and not-technically accurate answer is the slice thickness on a axially symmetric scan ( like most scans in rodents) is to enhance signal-to-noise ratio (SNR) while preserving the majority of anatomic detail. This is not so different that brain slice preparations that are used in electrophysiology measures of brain activity in neuronal layers or active centers. Most of the rapidly varying changes in cell structures are in planar direction - again - this is a generalization as we can find areas in the rodent brain were you have a lot of changes in anatomy and function along the longitudinal body axis.
The technically accurate reason for the slice thickness issue is the MRI slice is not perfect. It's actually much easier to make very thin slices but the SNR becomes very low. An MRI slice profile is a function of the shape of the radio frequency (RF) pulse shape and length and while we approximate a rectangular or box-car shape pulse it is most certainly not that. A number of factors come into play to form the slice shape which I can recommend a couple of good treatments on if you are interested.
The in-plane resolution for most MRI results are based on Fourier encoded image response which has a analytical model for describing its response and contents. This forms a rectilinear signal response grid with provides more image detail. So we choose to us this part of the well described image formation on the most interesting anatomy for our image experiment.
Of course, I started this explanation talking about axial images but we use the same thought process for sagittal and coronal/transverse image formation in rodents (and other animals especially if they have a right-left symmetric brain which is true for all vertebrates).
I'm including a URL from a colleagues lab describing this issue for slice selection - https://larsonlab.github.io/MRI-education-resources/RF%20Pulses.html
If you have any questions about the above explanation I'll try to answer them.
Cheers - Doug Morris
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