Computation of mean global and regional FA


Hello MRTrix team,

I want to compute global or regional mean FA for some subjects (as a single scalar for each subject). I know how to generate FA map for each subject using tensor2metrics command. However, what is the best way to compute mean FA in the whole brain or specific regions using the FA map?


Hi @Sepehr_Mortaheb,

The mrstats command is used to compute various statistics within an image, such as the mean. If you do not want the statistics to be calculated throughout the entire image, but only within specific voxels (e.g. the brain white matter, or voxels within a specific pathway of interest), then the -mask option within this command should be used.

As far as what mask should be provided and how it should be derived, this is entirely up to you as the experimenter. For instance, you can draw a mask manually using the mrview ROI tool, you can use a combination of tractography / mapping streamlines to underlying voxels / application of a threshold to highlight some subset of voxels, you can use any manner of brain / white matter extraction, registration to a template image & transformation of atlas masks back to subject space, etc…