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

Paulo Mint Labs paulo at mint-labs.com
Tue Nov 24 12:03:49 EST 2015

Hi Rob,

Normally we prefer to do everything on the dMRI space: intuitively it's
'better' (less noisy) to register a scalar image into the complex dMRI,
than the other way around and have to interpolate the dMRI. What we
typically do however is to resample everything to 2mm isometric, so
normally the T1 goes more coarse, and the diffusion gets a bit finer
And anyways, we always like to generate QA screenshot reports to quickly
check all went well.


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On Tue, Nov 24, 2015 at 3:38 PM, Reid, Robert I. (Rob) <Reid.Robert at mayo.edu
> wrote:

> 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
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