Hi Saad,
Turns out there were other bugs in that script that lead to the new bvecs
file not being output properly so I just went back to using my version of
eddy_correct that has the code in it already.
Interesting thoughts about when to use or not use bvecs rotations.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Saad Jbabdi
Sent: Thursday, January 28, 2010 7:18 AM
To: [log in to unmask]
Subject: Re: [FSL] eddy_correct and rotation of b vectors
Hi Ed and Niklas,
This is not actually quite true:
1. if you want to extract the rotation component of the FLIRT matrix,
you need to use avscale.
2. FSL4.1.5 has a script that does all that for you. It is called
rotate_bvecs, and it is based on a donation from Martin Kavec.
Unfortunately, it has a little bug. If you want to use it you will
have to edit the text and replace "done" with "fi" at the beginning of
the script (when it is testing whether it is going to over-write the
ouput file). Sorry!
Cheers,
Saad.
On 28 Jan 2010, at 13:10, Niklas Stein wrote:
> Hi Ed,
>
> there has been some discussion regarding this issue. Since
> eddy_correct
> uses motion correction with 12 dof, rotation (as well as shears,
> skews) is included. You can easily rotate the bvecs by applying the
> top left 3x3 submatrix of each 4x4 matrix in the .ecclog file to the
> corresponding bvec. This can be performed either in Matlab or - with
> sufficient experience - e.g. a shell- or perl script.
> AFAIK, in FSL this is, however, not yet implemented.
>
> With all due respect,
> Niklas
>
> Ed Gronenschild wrote:
>> Hi,
>> I'm wondering if in eddy_correct the motion correction also
>> involves rotation. If that is the case than also the b vectors
>> should be rotated.
>> Ed
>
>
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Saad Jbabdi
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