Calculating X,Y,and Z diffusion values from tensor?


I am interested in calculating the DTI-ALPS metric in some data using mrtrix. This essentially consists of getting the x, y, and z diffusion diffusion values into standard or template space and then extracting these tensor values out of ROI’s in specific tracts.

Would I be right in assuming that I could use the tensor2metric command with the -vector/-value flag to get an x,y,z diffusion images? What other flags or specifics of the command would I need to get x,y, and z, or V1,V2, and V3 from a tensor.mif file?


Hi @CallowBrainProject,

Assuming you’re after the eigenvectors & eigenvalues, yes. You can use the -num option to get specific ones, or all of them (e.g. -num 1:3) – they’ll then be concatenated in the output file. You can also have the eigenvectors modulated differently using the -modulate option – by default, they’re modulated by the FA, but you may prefer to get unit eigenvectors (-modulate none) or eigenvectors scaled by the corresponding eigenvalue (-modulate eigval).

The eigenvectors are computed with respect to the scanner / world coordinate system, by the way. Not sure whether that matches what you call ‘standard space’ though…

All the best,