Hi Saad, thanks very much for your advice,
Siewmin
Hi Siewmin (and I guess this should answer Sid's questions as well),
>
> If you run FSL's eddy_correct on your data, then this will, as you
> know, produce a text file called blah.ecclog
> You can then use the attached matlab script which will read your
> ecclog file and bvecs file, and apply the appropriate rotations to
> your bvecs.
> The top-left 3x3 of the flirt matrices do not only contain rotations,
> so you need to do a little trick to extract the rotation part (this is
> done for you in the matlab script attached).
>
> In my experience, I did not notice a huge difference in my data when
> comparing e.g. FA before and after bvecs rotation, but I guess it
> might make a difference on other data...
>
> The relation between the amount of bvecs rotation and the output of
> dtifit and/or the end result of tractography is not straightforward,
> so I am not sure you can objectively assess whether a correction for
> the bvecs rotation is necessary or not just by looking at MCFLIRT
> results.
>
> Cheers,
> Saad.
>
>
>
>
>
> On 28 Feb 2009, at 01:40, Siewmin Gan wrote:
>
>> Hi, I have a couple questions about this procedure which I came
>> across in the discussion
>> forum.
>>
>> I have 2 repetitions of the same DTI sequence to increase the signal
>> gained. I have
>> concatenated my bvals and bvecs and ran eddy_correct on the merged
>> file ( lining the
>> brain s up with the -t option in fslmerge).
>> It is recommend in the post here to " then rotate the bvecs by the
>> rotation part of the flirt
>> transformation matrices that are stored in the ecclog. I think you
>> should be able to
>> do this by simply multiplying each bvec by the top 3x3 matrix in the
>> flirt matrix for that volume"
>>
>> May I ask if you mean multiply each bvec number by the TOP LEFT 3x3
>> matrix as there
>> are 4x4 matrix in the ecclog for each volume?
>>
>> Secondly would this step be mandatory and would it be less accurate
>> in my
>> DTIFIT/BEDPOST procedure if I did not rotate the bvecs as mentioned
>> above? It is noted
>> on the email post that it is presumed the two brains are at
>> different angles at each
>> repetition of the sequence. How much motion would be required (from
>> one repetition to
>> another repetition) to do this above step of rotating the bvecs?
>> Visually when I check the
>> B0 images from each repetition, some subjects have a noticeable
>> shift in between the
>> repetitions while others has same positioning of the brain in both
>> repetitions.
>>
>> I used the MCFLIRT function on the FEAT option to check the level of
>> motion in the merged
>> file. The rotation is upto 0.04 rad and the translation 2-5mm. It
>> mentioned high level of
>> motion detected with the merged file. Is the rotation more important
>> than the translation
>> movement detected, to decide if I need to perform this step of
>> multiplying each bvec by
>> the 3x3 matrix in the ecclog for DTIFIT/BEDPOST procedure?
>> If the pre-stats report did not have high level of motion detected,
>> would it be safe to
>> concatenate the same bvecs (without rotating) to do the the DTIFIT/
>> BEDPOST procedures
>> required for tractography analysis?
>>
>> Many Thanks in advance
>>
>> Siewmin
>>
>
> Saad Jbabdi
> Oxford University FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222545 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
>
>
>
>
>
>
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