Hi,

I have successfully used DKE on a Mac (10.10.5) to reconstruct DKE metrics. I would now like to take the estimates from the DKE and utilize my FSL TBSS pipeline to run statistical analyses. Here is what I'm doing.

Data were converted from DICOM to NII using mcverter from University of Oregon

(0) the data have a qform and sform of "Scanner Anat" 
(1) taking native space DKI data set and running through FSL DTIFIT to get a FA map. 
(2) use the native space FA map (I'll call it FA_FSL) to run TBSS with my two cohorts
(3) use DKE on the native space DKI data set to calculate metrics (KFA, KMEAN etcetera). I have DKE resample to 1.5mm isotropic 
(4) I now want to take the TBSS derived warps and apply them to the DKE data. 

This doesn't work. It appears that the qform and sform are change by DKE to be in "Aligned Anat" with diagonal qto_xyz and sto_xyz matrices. 

If I do a "Check Reg" in spm, the images show they are aligned.

If I try to a FSL/flirt realignment without resampling/reslicing, specifying rigid body (dof = 6), they affine matrix is the identity matrix

If, however, I try to do a flirt resampling/resclicing using the identity matrix, the resulting image is all skewed with respect to the original b=0 image.

And of course, if I apply the warping, that is also messed up.

Robert