Fixel Averages


I’m wondering if there is a way for me to extract the average values of FD, FC and FDC for individual fixels in an analysis, or generate a heat map of these values. When using fixelstats I’m given the std_dev.mif file, but I’m unsure how to interpret these values without knowing what the average fixel metrics are (i.e. is 0.05 a high standard deviation for FD?). Is this information contained in the std_effect.mif file, or is this something else?

Thanks in advance!


Assuming all fixel images share the same direction and index information, you can use mrmath <fixel_image> ... <fixel_image> mean mean_fixel_image.mif to calculate fixel-statistics from the respective fixel contrast files. fixel2voxel converts fixels to spatial maps. You can look up the fixel format here.

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Thanks, much appreciated!

One small caveat with using mrmath on the fixel data directly is that the operations will be performed on non-smoothed data, as smoothing of the fixel data is performed internally within the fixelcfestats command. If you want e.g. group means on smoothed data, this can be extracted from the GLM beta coefficient values generated by fixelcfestats (even with the -notest option to avoid permutation testing), provided the correct understanding of what each of those coefficients encodes within the model.