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

[Luetzkendorf, Ralf]

Hi Donald,

thanks for the quick answer.

And its also normal that the B0 direction change like this...not only the b-value?
I mean 0.5 0.5 0.7 is okay to use as the B0 direction?

Another problem would be, that Im using FSL to register and afterwards recalculating the directions with the Matrix.
But I think that should work on the MRTrix directions the same way. The Rotationmatrix should be the same.

Thanks for the help,

cheers Ralf.



+++++++++++++++++++++++++++++++++++++++++++++++
Ralf Lützkendorf
Department for Biometry and Medical Informatics
University of Magdeburg, Germany
phone: +49 391 67 13546
fax: +49 391 67 13536

________________________________
Von: Donald Tournier [jdtournier at gmail.com]
Gesendet: Mittwoch, 2. April 2014 16:30
An: Lützkendorf, Ralf
Cc: \mrtrix mailinglist ‎[mrtrix-discussion at ww
Betreff: Re: [Mrtrix-discussion] direction Scheme - bvecs - encoding.b - diffrence - Siemens MRI Scanner

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<mailto: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 Engineering
King'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
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