Hi Robert,

Great to hear that DKE runs successfully in the latest build of Yosemite.  In my experience in using DKE (version 2.6) and TBSS, I have always started the processing from the straight dicoms.  [Or alternatively, generated a nifti from the dicoms (DKI sequence, DKI B0 sequence) using dcm2nii, found in MRIcron]

If you are using the DKE GUI, you don't have to presort your dicom folder with different sequences, as the GUI will display the different sequences to be used for processing in the folder that you specified for the GUI to load from. I bring this up due to the fact that DKE by default will generate the standard 7 metrics (3 diffusion, 1 FA, and 3 kurtosis) among others.  The key is this generated FA map that DKE gives us for each subject.

It is this FA map for each subject that I feed into the standard TBSS pipeline.  In my opinion and experience, I believe it is unnecessary to go through the trouble of of using the extra tools in FSL to obtain the FA map that you specified.  The reason is because if you use the FA map that is generated from the DKE processing, it will be in the same space as your output diffusion and kurtosis maps.  Which in the case of TBSS, it will take care of all normalization and coregistration for you anyways based on your template or option that you are choosing (tbss_2_reg tbss_3_postreg).

Furthermore, if you are looking to normalize all the FA maps to same space and subsequent non-FA maps (kmean, krad, dmean, etc...), FSL's TBSS also takes care of that for you in their standard pipeline.  If you are following the TBSS standard pipeline Steps 1-4, once you use the FA maps and other non-FA maps, there will be a stats folder generated that contains the 4D nifti files for your metrics such as: all_FA.nii.gz; all_kmean.nii.gz; all_krad.nii.gz; etc.  These 4D files contain all of the subjects metric map concatenated into one file with normalization and coregistration taken care of into MNI space.  From this 4D file where each time series corresponds with one independent subject, you can then use FSL split to retrieve the independent 3D nifiti.  TBSS can be tricky when using non-FA maps due to the file directory organization.

To wrap it up though, this is my standard pipeline of processing of utilizing DKE to output my metric maps of interest, and using them in a TBSS analysis, hope that provides some clarity in using TBSS.

Cliff