Dear Rob,
>
> We would like to correct EPI distortion in diffusion MRI *and* minimize blurring from resampling. There are several ways to correct EPI distortion, depending on what other images are available (e.g. flipped phase encoding or undistorted T2w -> topup, T1w -> BrainSuite), but the results fall into two distinct camps of being in either the T1w space (high resolution) or undistorted dMRI space, which mainly means dMRI-sized voxels. Our analyses often combine the dMRI and T1w images in some way, but we usually have a choice of registering and resampling the dMRI images to the T1w images, or the T1w images (or segmentations, or atlas regions) to the dMRI images. Both ways work, but presumably one of the spaces is better to work in. Does anyone have experience with using both low and/or distorted images (dMRI) and high resolution undistorted images (e.g. T1w) together, and have any insights?
>
> Theoretically each additional resampling step introduces some degradation, so "native" space is the right one for dMRI.
> However,
> * The T1w voxels are so much smaller than the diffusion voxels that the resampling of dMRI into T1w space is typically excellent.
> * The undistorted diffusion images *are* resampled, so they are not really in native space. If resampling is necessary it is better to resample finely (i.e. use T1w space). On the other hand, many parts of the brain, like the parietal lobe and motor-sensory strip, are relatively unaffected by EPI distortion and may be left in nearly native space after undistortion with topup, if head motion and eddy current distortion are not a large problem.
you are right that for a typical diffusion data set the movement and EC distortions are such that after resampling one can pretty much assume that very few voxels have ended up on the original voxel centres, and that most voxels will have been resampled.
Given that and provided that one eventually want to work in a higher resolution space it would make sense to be able to do that resampling in a single step. Currently topup (or eddy) cannot do that. There has been local requests for such functionality so it is possible that we will provide it in the future.
It should also be noted that for example probtrack knows how to interpret warp fields and transformation matrices so you can effectively do your tractography in the resolution of your T1 (or standard brain) without the need to resample the diffusion data into that higher resolution.
Jesper
>
> We look forward to reading your opinions,
>
> Rob
>
> --
> Robert I. Reid, Ph.D. | Sr. Analyst/Programmer, Information Technology
> Aging and Dementia Imaging Research | Opus Center for Advanced Imaging Research
> Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org
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