I would use the participants own bvecs, particularly if you are doing tractography.

The bvecs file has the information about which way the diffusion gradients were pointing. The calculated directions of the eigenvectors (and hence the direction of the calculated tracts) depends on the direction of the gradients relative to the patient.

If there are only minor differences in the bvecs, then there will only be minor differences in the results. But you don't know that there are ALWAYS only minor differences. So to be on the safe side I would go with the patients bvecs.

I guess it would be interesting to find out why the differences exist. It might depend on the position/ angulation of the subjects head

Although, assuming it is the same MR sequence for everyone, the calculated MD and FA should be the same, since they are not telling you about specific directions. 

Dear Michael,

Thank you for your comments! You were right regarding head positioning; I came across a tutorial which stated:

"Ideally these gradient directions should be the same for every subject across the study. However, due to head placement in the scanner, the exact values of these gradients may vary slightly subject-to-subject". So bvecs  seems to vary due to head positioning. The tutorial also suggested that one use the individual bvecs files. Thanks!

-Lasse

Dear Lasse,

to simplify fsl - dti analysis and motion correction, especially when there are many subjects to be analyzed, you can consider using scripts and rotate bvecs.

Best regards

http://blog.cogneurostats.com/?p=302

http://dbic.dartmouth.edu/dti/DTIGuide.pdf

thank you Riccardo!