I would like to ask if it’s possible to generate tractography where you can use FA to map the values that fall within the streamline, for visualization? I would like to view the streamlines where I can map their FA values through the specified color map intensity. I tried tckmap but maybe I’m doing it wrong.
the code is something like this.
tckmap tract.tck -contrast scalar_map -image FA.mif -template FA.mif tcktract.tck
-it says .tck file is not possible. What file type should be the output?
Thank you so much in advance.
tckmap deals with “mapping tracks” to a voxel grid for the sake of producing data on that voxel grid. What you’re looking for is “taking samples along tracks” based on data stored on a voxel grid.
You say sem-eah-ntics, I say sem-uhh-ntics?
(We have literally spent over a decade agonising over command names…)
Since you’re specifically wanting to store an FA value per streamline vertex and utilise that information in
mrview, you want to not use the
-stat_tck option in
tcksample (which reduces things to a single scalar value per streamline), and you want to write the result in the
.tsf format, which the
mrview Tractography tool will happily use to determine vertex colours.
Thank you so much. It worked!