Tractography with scalar/tckmap

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.

Welcome Ashly!

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? :upside_down_face:
(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.


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Thank you so much. It worked!