Hi Megan

1) platform: Did you compile it yourself or download from NITRC? Apart from the FSL tools (bet2), the other tools should have come with the DTIPrep download, so those tools should be there. You can specify in the protocol where this tools are located.

2) to Slicer or not to Slicer: Both options are equally workeable, but the nice thing about the Slicer extension is that those external tools should be all setup (apart from the FSL bet). It may though be that we need to update the extension and it's not compatible with the newest version of Slicer.

3) Those additional tools are necessary for a) mask creation and b) tensor computation. Thus, you will get the QCed DWI without the need for these tools DTIPrep did not find.

4) NIFTI: Best use the Slicer module DWIConverter (stand alone DWIConvert) , we use it regularly to take DTIPrep data into the FSL world (e.g. for probabilistic tractography).

5) Gradient sphere: did you enable the sphere and gradient display (click on the correspoding icons)?