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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