Dear Derek,
We would recommend that you do your analysis in the diffusion space and then transform your results to structural or standard space, rather than transform all the original data. For this reason I don't believe that Eddy can take an external template.
If it is essential that you transform your data, then you can rotate bvecs using fdt_rotate_bvecs, which is more generally used for corrections after motion and eddy current distortion corrections.
All the best,
Mark
On 12 Jan 2014, at 15:45, Derek Gong <[log in to unmask]> wrote:
> Dear FSL professors,
> Hello!
> I met some problems in analyzing dMRI data.
> Our data contains DTI images which voxel size is 2x2x2 mm with 64 gradient directions(3 b0 images before them, so in total there are 67 diffusion images in DTI data), and T1 images in 1x1x1 mm voxel size.
> For each subject, I normalized his T1 image to MNI152_T1_1mm by using FSL FLIRT first. After that I got standardized T1 image. Then I registered 67 diffusion images to standardized T1 image respectively using FLIRT by Rigid Body(6 parameter model) transformation. After that I got 67 4x4 affine matrixes. The question is I don’t know that how to transform corresponding diffusion gradient direction values in "bvec" file to T1 space. Is there a more exactitude or elegant way to do that?
> And another question, I know Eddy script can correct subject movements. But I'am not clear that whether I can using custom template image as a reference image to do Eddy correct. And how to do that? Moreover, whether bvec would been transformed accompanied with movement correct?
> Thank you for your attention very much, and waiting for your reply.
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