Hi Ehsan,

I suspect that it has something to do with a difference in coordinate systems. I believe that the following is going on: bvecs_gtable.bvec is most likely the orientation of the gradient vectors in the coordinate system of the bore. This orientation is not necessarily the same as the coordinate system of your image. Normally what you do is extract information out of the dicom header called ImagePatientOrientation, and use the orientation of these axes to rotate your raw gradient table to the coordinate system of the Image. Dcm2Nii will also do this when you transform your data from dcm to nii for example. I have not worked with explore DTI before, although it looks like this transformation is applied to your gradient table as well.  Does the other text file you are working with provide you with any information on the orientation of the image in the scanner space? In dicom headers it is given as a 1x6 vector.  From the two gradient matrices you have, you should be able to calculate the rotation matrix between them. In matlab it should be something like R=B\A ?

Anyway, if it does not really matter where it comes from, I would run DKE with the bvec you created from the Bmatrix (provided you put it in the right format), because for tractography it is important that your gradient tables are expressed in the same coordinate space as your images.

Hope this helps,
Emilie