[Mristudio-users] update of gradient table in DtiStudio

[susumu mori]

Hi Luca,

There are several issues you raised;

1) Our MI algorithm: I forward this question to Kegang Hua who implemented
an algorithm written by Jinsuh Kim in Iowa U.
2) How the gradient table updated: There is an option to re-calculate
b-matrix if there is any rotation involved in the post-processing
registration (a check box with "adjust gradient table ...."), although my
lab is not using this function. It is my personal opinion that if a subject
rotates his/her head to a degree that this option makes a difference, there
should be so many other quality issues that can't be solved by
post-processing reorientation of b-matrix such as signal drop,
mis-registration of odd and even number slices within one 3D data,
through-slice rotation within one 3D data, etc. Also consider following
things;
> In regular data, the amount of rotations is usually less than 1 degree
within 5-10 min scan time
> With 5-10 min scanning, SNR is such that test-retest reproducibility of
fiber orientation calculation is about 3-5 degree
> I'm not sure if post-processing realignment algorithm has a precision of 1
degree for rotation detection, which is difficult to differentiate from
sheering.
> Eddy current sheering should not require b-matrix rotation
> If there are 3-5 degree rotation during scan, that data is very outlier
and I'm not sure if you want to salvage it by applying b-matrix
reorientation.
3) What does it happen with resampling: Any post-processing alignment leads
to pixel-interpolation and resultant blurring. This is a separate issue from
any resampling to enhance the resolution. The post-processing realignment
can be done without changing image resolution.

Susumu

On Mon, Dec 27, 2010 at 3:38 AM, <luca.binotto at unipd.it> wrote:

> Hello Susumu,
>
> I would like to know something about the way DtiStudio performs the update
> of the gradient table after the realignment of the dti dataset with
> respect to the mean_b0  volume.
>
> The registration algorithm implemented in DtiStudio using mutual
> information (MI):
> 1) does it uses normalized mutual information or which other formulation ?
> 2) how is the gradient table updated ? (rough simple theory)
> After realignment of the DWI volumes, b-matrix (the gradient table) must
> be updated.
>
> Patient motion and eddy currents can cause errors in the calculation of
> parameters that describe diffusion in each voxel of a DWI dataset.
> In normal conditions eddy currents contribution should be
> very small (< 1% ?).
> But the b-matrix (gradient table) is calculated with respect to a fixed
> coordinate system (at the acquisition time) so the b-matrix must be
> rotated accordingly to the transformation applied for image registration
> otherwise we should get poor fiber statistics and some fibers possibly
> deviate.
>
>  So the gradient table is affected  by rotations. Translations don't
> change it.
>  But what does it happen with resampling (applying a scaling factor: es.
> affine transformation) to a dwi dataset?
>  According to you is normally its effect small (as for eddy currents
> effect) or can be more important?
> For example a scaling factor such that a volume with a voxel size of
> 2x2x2 mm3  is resliced to a 1x1x1 mm3 voxel size can be important its
> effect or "only" a lower image quality (eg. I read somewhere of a
> "red background" superimposed to the correct color map)?
>
>
> thanks in advance,
> best regards,
>
> Luca
>
>
>
>
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