[Mrtrix-discussion] direction Scheme - bvecs - encoding.b - diffrence - Siemens MRI Scanner

[Donald Tournier]

Hi Ralf,

I'm assuming you're supplying your own DiffusionVectors file, and comparing
them to the MRtrix directions read from the DICOM headers? If so, this is
normal, and is due to a difference in the conventions used: DICOM uses a
LPS reference frame, whereas MRtrix (and NIfTI) assume a RAS frame. That
should mean that the X & Y components are reversed between the two.

As to the b=0 no longer being zero, this is most likely due to the online
calculation of the effective DW scheme taking account of the imaging
gradients. The system applies the right DW gradients, but computes the
b-value and gradient direction based on *all* gradients between excitation
and echo. You'll get a small non-zero b-value even if you specify b=0 due
at least to the crushers around the 180° refocusing pulse(s). You'll
probably also find that your DW scheme changes slightly with different
slice orientations, due to the different orientations of the imaging
pulses...

Cheers,
Donald.



On 2 April 2014 10:50, Luetzkendorf, Ralf <Ralf.Luetzkendorf at med.ovgu.de>wrote:

> Hi to all,
>
> I have a little problem with the vector scheme.
>
> I noticed a sign difference between the scanner directions, that I fill in
> and MRTrix reading out from the data.
> Even if Im measuring straight axial, like the documentation said.
> I hope that is normal.
>
> Is it okay to use them both or should I ever use the directions that
> MRTrix is gathering from the data?
>
>
> Now I have a second problem. I used the same direction scheme like before,
> but now MRTrix doesnt only change the signs.
> It has different values for every B0 data set. The other values are still
> the same.
>
> The B0 direction looks like that:
>
> 0.5 -0.5 0.707107 5
>
> instead of:
>
> 0 0 0 0
>
>
> Did somebody encouter the same problem? Which should I use?
>
> I hope somebody can help,
>
>
> Cheers Ralf
>
> +++++++++++++++++++++++++++++++++++++++++++++++
> Ralf Lützkendorf
> Department for Biometry and Medical Informatics
> University of Magdeburg, Germany
>
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>



-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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