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FSL  May 2011

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Subject:

Re: eddy_correct affine registration

From:

"Dr T.M. Rolheiser" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 20 May 2011 16:31:31 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (77 lines)

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.
>>> 
>> 
>

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