Hi,

I just ran few subjects with DTI prep and computed the mean absolute RMS motion using FSl. I compared the mean absolute RMS motion before and after DTIprep. But strangely for some subjects the mean absolute RMS motion was higher for subjects after DTI prep.

Any thoughts why is it so?

Thanks

I assume you meant FSL (using fsl_motion_outliers)?

Not sure how the RMS motion is computed, and this could be an artifact of the particular program you are using to compute the motion. If there were such a thing as a perfect way to measure motion, we would simply use that measure as a goal to optimize. But any measure introduces a bias to its assumptions.

But it is certainly not impossible for DTIPrep (or any motion correction, such as in FSL) to make things worse. Especially if there is no motion present, a registration process (to correct the potential motion) may correct for a larger motion than actually present (due to the high noise, low SNR). 

Martin

Hi
I have a related question.
With the rot_bvecs script one can adjust the bvec gradient orientations to the applied motion correction and eddy current correction in the eddy_correct script.

Is there a way to do the same with DTIPrep--i.e., adjust the gradient vectors according to the applied motion correction?
Originally posted by Martin Styner:

All motion and eddy current correction is automatically applied to the diffusion gradient directions, i.e. DTIPrep does not save any DWI information that does not have a correspondingly corrected gradient direction. Thus it does not offer an option to separately apply the motion or eddy current correction.

Martin

Thanks very much