Hi experts,

For my fixel-based analysis study I am trying to visualize the mean FDC at particular tracts as percent reductions from the control group mean in a bar plot, similar to what Zarkali et al. did for their 2020 Neurology paper, and what Mito et al. did in their 2018 Brain paper. I had a question about how the authors extracted the data for making these plots.

From my understanding and based on how I set up my design and contrast matrices I first get the control group mean from adding the beta0 and beta1 files from the fixelcfestats output. I then calculate the percent effect for FDC in the patient group at each tract by dividing the absolute effect by the control group mean and multiplying by 100. Then I threshold this percent effect by each tract mask that I obtained from registering an atlas to my population template space, performing masked tckgen at the tract of interest, and using tck2fixel to get the corresponding fixel mask at that tract, and then I output the mean percent effect. I was wondering if this is the correct way to go about plotting these mean percent reductions, because I wasn’t sure about how I could calculate the confidence intervals at each tract with the percent effect for all patients relative to the control group like what Mito et al and Zarkali et al did.

Thanks for all your help!