The format for the bvecs is described here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT
Cheers
Saad
On 12 Dec 2012, at 12:14, Christopher Parker wrote:
> Hi Saad,
>
> My mistake, I misinterpreted some other descriptions. Thanks, I found the script. Can I just clarify that the b-vectors should be in a file as:x_vec1 y_vec1 z_vec1 x_vec2 y_vec2 z_vec2 etc. format? Ie with no spaces in between x y and z or different gradient directions?
>
> Best,
> Chris
>
>
>
>
>
> - - - - -
> Hi - I hope this is not common practice! You need to restore geometry (put the data in the right place) which you can't do by simply changing the bvectors.
>
> I guess you are referring to rotating the bvectors *after* eddy current correction to account for head rotation. You can do this with fdt_rotate_bvecs, which should be part of the soon-to-be-announced FSL502, or you can find the script in previous posts.
>
> Cheers
> Saad
>
>
> On 10 Dec 2012, at 16:12, Christopher Parker wrote:
>
>> Hi FSL,
>>
>> I would like to perform eddy current correction on my diffusion data. As I understand the tool "eddy_correct" performs this correction by affine registration of all volumes to the b=0 volume. However, it is common practice to apply the transformations to the b-vectors instead of the actual volumes. Is there an FSL function to do this?
>>
>> I could possible code this myself if there is not function. I could use the .ecclog file to provide the transformations. Is anyone clever enough to know how to apply a transformation from the .ecclog file to one of the gradient vectors? Is this a simple matrix multiplication?
>>
>> Best,
>> Chris
>>
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
|