Hi Maedoc, diffusion modeling outputs (diffusion tensor, ODFs etc.) are always saved in T1-space. So, usual tractography would results into tracks being generated and saved in T1-space. An exception to this would be if diffusion outputs from diffusion_coord_outputs directory is used for tractography (this directory is only generated if --output-diffusion-coordinate flag was used).
As a interesting twist, one has to apply the inverse of the affine w/o translation, i.e. just the 3×3 not 4×4 affine.
Above statement is not entirely accurate. BDP supports wide variety of data transformation across T1 and diffusion space, and so users do not have to do it themselves. Please take a look at “TRANSFORMATION FLAGS” section on flags documentation, in particular flags: --transform-t1-volume, --transform-interpolation, --transform-data-only. This is the recommended way to transfer data from one space to another.
Flag documentation: http://brainsuite.org/processing/diffusion/flags/#fullflaglist