Hi Darius,

First, a few notes that may or may not apply to your project.

Note 1: I am not sure how committed you are to using JHU regions. If you want to conduct ROI analysis in white matter, you may want to use connectivity-based ROIs instead of the anatomically-defined JHU ROIs that may contain very different connections. The track-density images corresponding to the different edges of the connectome can be converted to masks (one mask per edge), transformed to the space of individual subjects, and used to extract average values of different MRI properties per edge.

Note 2: You mentioned you want to perform tractography on the IIT atlas. Note that the tractogram is already provided. Of course you can redo tractography on the HARDI template using your preferred approach and parameters.

Now to your questions:
The space of the IIT atlas and the ICBM152 space do not perfectly match. You should register one space to the other. If you do that, can't you apply the resulting transformation to the JHU regions to bring them to IIT 256x256 space?
Also, how did you apply the linear transformation?
Finally, if the above do not spark any ideas that lead to solutions, can you share a screen shot so that we get a feeling of the kinds of problems you have encountered?

Take care,
Konstantinos