Hi Rowena,

I think the jhu labels are in 182 space (not 256). As a result, the output of DTI-TK using our 256 atlas will most likely not work with the jhu labels. I should mention here that you may want to take a look into the "HOW-TO-use-the-WM-atlas". The IIT white matter atlas contains four-dimensional (4D) white matter labels. This means that each white matter voxel is assigned a list of gray matter label-pairs with the most probable connections through that voxel. The reason behind the 4D labels is that multiple fiber populations often share the same voxels, and therefore white matter voxels must be given the chance to have multiple labels. If you still prefer the winner-takes-all approach (similar to the jhu approach) then you can simply use the top label in each voxel of our atlas, which means you can simply use the first volume of our 4D atlas and ignore the rest of the volumes (less likely labels). However, I recommend avoiding "winner-takes-all" white matter atlases, for the reason explained above. It is best to embrace the truth i.e. multiple connections can share the same white matter voxels, so each white matter voxel should have multiple labels.

Please let me know if you have more questions.

Regards,
Konstantinos