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This sounds pretty good so far. I will probably try to change the script by adding -dof 6, because then I could use the rotbvecs script (which depends on the .ecclog file) to alter the bvecs based on head motion only. This is a really helpful discussion board... I ought to do this more often. Thanks a bunch... Tyler On May 20 2011, Stamatios Sotiropoulos wrote: > Eddy correct just calls flirt. You can run flirt instead of eddy_correct > through the command line and specify the settings you want to apply. > >Cheers, >Stam > > >On 20 May 2011, at 16:01, Dr T.M. Rolheiser wrote: > >> Thanks for the quick reply, >> >> I suppose the underlying issue is that I would like to correct bvectors >> for motion, but not for eddy currents, and if eddy_correct does both in >> a way that can't be separated, then I'm not sure whether it is prudent >> to employ a bvector rotation. >> >> The raw data is of very good quality, and the preprocessed images >> always look very good so perhaps this is less of a problem, and more of >> a curiosity. >> >> Is it possible to have eddy_correct simply use the 6-dof procedure? >> Would this involve changing the code? >> >> Thanks again... >> Tyler >> On May 20 2011, Stamatios Sotiropoulos wrote: >> >>> Hi Tyler, >>> >>> 1) Eddy_correct is based on a simple model for eddy current artifacts >>> that include scaling, translation and shear of the images. All these >>> artifacts, including head motion can be captured by an affine >>> transformation. That's why eddy_correct uses 12 DOFs rather than 6, >>> which would only correct for head motion. >>> >>> 2) The link "FDT theory" on the FDT webpage describes how bedpostx and >>> probtrackx work. For dtifit there is no much theory, it is a simple >>> least squares fit of the linear DTI model. Peter Basser's first DTI >>> papers (any many other review papers since then) have all the >>> information you need. >>> >>> Hope this helps, >>> Stam >>> >>> >>> >>> On 20 May 2011, at 13:02, Tyler wrote: >>> >>>> Hello FSL Kingdom, hopefully someone can help me out with two >>>> specific questions. 1) Regarding the naming and function of the >>>> command eddy_correct: If all the command does is register the >>>> diffusion images to the reference image (12-degree of freedom affine), >>>> can this be considered an eddy-current correction? Granted it is >>>> important to align the diffusion images to a reference image before >>>> fitting a tensor, but how would one directly address the issue of >>>> correcting for eddy distortions independent of head motion? Does FSL >>>> have this capability? 2) As a secondary question, where can I find >>>> more detailed information about the FDT pipeline? The general >>>> information on the fsl webpage doesn't really provide enough >>>> information about the tools (e.g., how does the dtifit command >>>> calculate the FA/MD images). PS: I'm sorry if these posts have already >>>> been covered... I searched the archives but didn't come up with a >>>> direct answer. >>> >> >