[Mristudio-users] Gradient tables and SPM coregistration

[susumu mori]

Hi Dorian,

We don't have experience in mixing SPM transformation and MriStudio
pipeline. In general, you have to be very careful to mix pipelines from
different sources;

1) coordinate systems could be different; right-hand or left-hand
coordinates / neurology or radiology orientation. You have to be careful so
that the images and transformation matrices are in correct orders.
2) gradient vector re-orientation: If you touch raw diffusion-weighted
images, you have to transform the gradient vectors too. This is not
difficult when you use linear transformation, but if you are using
non-linear transformation, each voxel has to have its own gradient table.
The procedure becomes simpler if you transform images after tensor
calculation, but if you transform a tensor field, you need to make sure to
re-orient the tensor in each voxel.

In general, each software (FSL, SPM, MriStudio) should be already tested
for the consistency for these issues in a transparent manner, but once you
mix the pipeline, such a consistency may be lost.

Susumu

On Wed, Dec 26, 2012 at 12:16 PM, Dorian P. <alb.net at gmail.com> wrote:

> Hi everybody, and happy holidays,
>
> I am using DTIstudio in a complex workflow.
>
> First, I need to make a nonlinear registration using masks on lesioned
> data. SPM is doing a good job at this point. To apply the transformation
> matrix produced by SPM, I must export images from DTI studio (analyze
> format), apply the deformations in SPM and import the files back to
> DTIstudio. However I am not sure whether a problem arises with the gradient
> tables not being the same any more. How can I apply the transformation
> matrix from SPM? Is there maybe a way to convert .mat files to .vtk and do
> all transofmrations in DTIstudio/Diffeomap?
>
>
> Second, having both T1 and b0 images in two different sessions, which one
> is better in theory for registration, T1s or B0s ? In many examples the b0
> has been used for linear (AIR) and nonlinear (LBBDMM) registration. But on
> the other side a b0 is acquired in a fraction of the time of a T1, so may
> be less stable to artifacts (or with fat artifacts?).
>
> Thank you.
> Dorian
> TJU
>
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