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As noted by the previous post, there are several scripts to rotate bvecs out there. I would go for the HCP pipeline one (https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/Rotate_bvecs.sh), although the result should be the same.

I would not recommend upsampling the diffusion MRI data. This will lead to a file that is ~8 times larger, which will cost greatly more memory and will make running qboot 8 times slower. In the end this file will not contain any additional information as if we run qboot on the original 2x2x2 mm resolution data. So, instead I would recommend to transform the mask to diffusion space rather than going the other way around. You can use epi_reg or flirt to get the transformation matrix to move the mask to diffusion space. Your mask will lose resolution in this process, however in the end this simply reflects that the data you want to mask has this lower resolution.

Michiel

On 17 Jun 2019, at 15:45, Melanie Spindler <[log in to unmask]> wrote:

Dear FSL experts,

I want to align (intra-subject) a DWI with an AC-PC oriented T1 image.
Epi_reg seems to be a good choice for that, but as far as I know I should rotate the gradient table after that.

I first process the DWI with topup and eddy, and then use epi_reg.
I know that eddy rotates the bvecs for me, but I think they have to be rotated again after epi_reg? How would you do this?
epi_reg also creates a new file with the same dimensions as the T1 (resulting in upsampling from 2x2x2 to 1x1x1). Is this advisable, or is there a way around this?

(Background: I would like to match a mask created with the T1 image as closely as possible to the DWI to run a clustering algorithm (on ODFs created in qboot). A better spatial resolution would of course help with that.)

Thank you in advance :)
Cheers
Melanie

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