Hi Loic – In simple terms, motion will cause a rigid transformation of the brain (translation and rotation only), whereas eddy currents will add non-rigid effects (scaling/stretching). By registering each DWI to the first b=0 image, and then extracting the translation and rotation part of the transformation, you isolate the part of the transformation that’s due to head motion. The rest of is due to eddy currents.

Best,
a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Daumail, Loic Jean" <LDAUMAIL@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, July 11, 2018 at 10:11 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] [TRACULA] eddy_correct /affine registration matrices / motion/ eddy currents

Dear FreeSurfer experts,

I would like to understand better the principle of eddy_correct: 

-in which way the eddy currents caused by motion are set apart from the eddy currents caused by fast switching diffusion-encoding gradients? 

-and then, how are the affine registration matrices reflecting motion computed  by eddy_correct considering the previous issues?

-does eddy_correct even computes these affine registration matrices(dwi.ecclog)? or is it another tool of dmri_motion? 


Thanks,

Loïc Daumail
Graduate intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST