Good afternoon TBSS experts,
I am in the process of performing quality assurance on a set of diffusion imaging data on which I plan to run a series of TBSS analyses. As I did not collect this data at the scanner myself, I am coming to realize that a large number of subjects had their superior cerebral cortex cut out of the field of view (FOV) with varying levels of severity. I've attached examples of mild, moderate, and severe FOV truncation affecting the superior cerebral cortex to this inquiry. The images are labeled accordingly.
Most of the tracts that I’m interested in are subcortical, or do not project to the superior cerebral cortex (i.e. fornix, uncinate, etc.). In light of this, I’m wondering if I can still use this data for whole brain TBSS analyses if I am willing to ignore the portion of cortex that has been cut off. However, my concern is that the error of having the superior cortex cut out of the FOV will cause an issue with the calculation of whole brain scalars as it propagates throughout the entirety of the white matter (WM) skeleton.
Might someone be able to tell the following?
Thank you in advance for all of your helpful insights!
Kind regards,
Linda
Hi Linda,
what I can see here is mostly a registration problem, as the calculation of the sample-specific template is crucial. Normally, the registration tools should cope with small FOV images, so checking and re-checking the resulting normalisation to MNI template space is quite important. Perhaps it could help, if you want another layer of complexity, to try DTI-TK tensor-based registration, if FLIRT-FNIRT isn't that successful in this case.
For all the other question: In my understanding the skeletonization is a local process, FA voxels are displaced in a local manner. That's why I don't understand your phrasing "whole brain scalars as it propagates throughout the entirety of the white matter (WM) skeleton". Statistics are running on a voxel level, too, so you just can interpret the FOV your data can provide.
Best,
Martin
Hi Martin Domin ,
Thank you so much for your thoughtful response. This is very helpful to me, and I sincerely appreciate your taking the time to explain this to me!
Kind regards,
Linda
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