Dear MRtrix team,
I hope all of you are well.
I am currently investigating changes in a paediatric cohort that underwent temporal lobe epilepsy surgery, both at a global connectivity level and individual white matter pathways. In particular, I have multi-shell data (13 interspersed b=0; b=1000 / 60 directions and b=2200 / 60 directions) before and after surgery, and I would like to use Fixel Based Analysis so that I could disentangle differences in specific white matter pathways. After having done all the required preprocessing (denoising, Gibbs ringing removal, Motion and Eddy/Susceptibility distortions and bias field correction) I still have a few remaining questions before proceeding and would really welcome your comments:
• First of all, I should note, that as I expect to find different changes depending if the operation was on the left or on the right (according to previous literature) I believe performing the FBA independently for left and right sided patients is the way to go; however I believe the response function should be fairly similar before surgery, so would I was thinking of using both left and right sided patient data to create a group response function (before surgery) prior to continuing the FBA analysis individually for left and right sided patients. I have also read in another post that I could use all of the data to create an group average response, but I have some reservations because of the different changes that can occur after surgery. Any comments?
• Secondly, I understand that one of the advantages of the FBA analysis is to benefit from FOD based registration which we can also use to register other data, independently for this analysis. However, I am concerned that attempting to create a population template including pre and post-surgical data will result in poor registration – do you have any experience in that? Alternatively, I was thinking of creating a template based (with ‘’‘population_template’’’) on the “intact” pre-surgical data (no resections) and then use transformations that I have derived from ANTS registration between pre and post surgical FA (using resection segmentation as a mask) to propagate individual FODs to the “intact” template space. Does it sound like the right way to go or would you try to do the initial template generation with all of the data (pre and post surgical together)?
• Thirdly, having seen first uses of longitudinal FBA analysis which applies to my case – timepoint 1 (before surgery) and time point 2 (after surgery) - I am still undecided whereas the best approach is just to do a “standard” FBA with pre and post surgical data in one template vs creating a “midway-point” template onto which I would project the individual FODs.
• Finally, I was wondering whether the data corresponding to resected areas should be kept or removed from the analysis, prior to running tractography on the fixel template (template and white matter masks). In voxel-based analysis I am expecting to see immediate changes in the regions surrounding the resection (as I have with TBSS) and so I removed the resected area, but with FBA, those changes might be more pronounced in the whole extent of the tracts and if I remove data I may change interpretation of the results…?
Thank you very much for all the work you put in these tools and your time spent in helping others!