[Neuroimaging] [Dipy] Should we resample dMRI to T1w, or T1w to dMRI?

[Reid, Robert I. (Rob)]

Hi,

My apologies if you've already seen this on the FSL mailing list - I'm trying to get a wide sample.

We are trying to decide on whether our lab's internal diffusion MRI processing should write its images in dMRI space or T1w space, and would appreciate your opinions.  The question is prompted by the EPI undistortion step, which necessarily introduces a resampling step of some sort, and tends to produce results in either T1w space (e.g. BrainSuite) or in DTI-sized voxels (e.g. FSL's topup).  Which algorithm we use depends on what other data we have (topup works best when pairs of images with flipped phase encodings are available, but usually they are not), but we would like to settle on a consistent format, and avoid resampling more times than necessary for our typical analyses.

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.  If a diffusion processing step is using T1w (for example, tractography often uses the T1w gray/white boundary to place seeds), it seems like the T1w image would be more damaged by going to DTI than the DTI would be damaged by going to T1w.
* 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.

Based on feedback I've already received, I should add that we will be doing quality control on the T1w <-> dMRI registration, and would fix, reject, or if necessary work around drastic registration failures.

We look forward to hearing from you,

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