R: Re: [Mrtrix-discussion] b-value correction

[Matteo Figini]

Hi all,

About eddy_correct: I have wondered what -nosearch means, too, and I found 
somewhere that it sets the angular search ranges to 0 just in a first step 
using a low-resolution version of the images. So I figure that eddy_correct 
does correct for motion, but assuming there is no large rotation.
However, FSL documentation is not clear about that and I can't remember where 
I found this information, so if anyone knows more I would like to know if I am 
right

Matteo

----Messaggio originale----
Da: d.tournier at brain.org.au
Data: 04/09/2012 2.27
A: "Mr Javier Urriola Yaksic"<javier.urriola at uq.net.au>
Cc: "mrtrix-discussion at www.nitrc.org"<mrtrix-discussion at public.nitrc.org>
Ogg: Re: [Mrtrix-discussion] b-value correction

Hi Javier,
Unfortunately there is no simple way to do this within MRtrix at the moment - 
this is something that we're working on, and will hopefully be included in 
future versions. In the meantime, if you're able to get FSL to rotate its bvecs 
file, you might be able to feed that to MRtrix by re-orienting and re-
formatting the resulting bvecs/bvals files into a format suitable for MRtrix. I 
don't have anything to do this right now, but maybe someone else might...?
However, there's a couple of issues I'd like to raise related to your post. 
First off, in our experience, eddy_correct does not handle high b-value, low 
SNR data very well. What we see is that the DW data are 'stretched out' 
(scaled) to match the b=0 image, to a varying degree based on the DW direction 
and the corresponding signal around the edge of the brain. We typically find 
that it introduces more artefacts than were present in the data - especially 
for data acquired using twice-refocused sequences, which are robust to eddy-
current effects (the default on Siemens scanners). That said, if you're using 
lower b-values around 1000s/mm², you might find it works fine - I can only 
recommend you look closely at the results before and after correction, we found 
for example that the FA map was much more blurred after correction than 
otherwise.
The other related issue is that as far as I can tell, eddy_correct is not 
designed to perform motion correction. Someone may be able to confirm this for 
me, since I can't really figure this out from the limited documentation. If you 
look at the eddy_correct script, you'll find that it splits the 4D file into 3D 
volumes, and calls flirt to realign each volume to the first one. The issue is 
that flirt is invoked with the '-nosearch' option, which according the 
documentation, "sets all angular search ranges to 0 0". I can only interpret 
that to mean that it will do an affine (scale, translation, shear), but no 
rotation, and so can't really be used for motion correction where non-
negligible rotations are expected. If someone has more information about this 
and can confirm one way or the other, I'd love to hear about it! 
Motion and eddy-current correction on high b-value data is tricky, and there's 
been a few abstracts on the topic at recent ISMRM meetings (Jesper Andersson & 
David Raffelt at ISMRM 2012, and -I think- someone from Yanniv Assaf's group at 
the 2011 ISMRM). Hopefully, we'll have something robust within the MRtrix 
pipeline at some point in the not too distant future...
Cheers,
Donald.

On 3 September 2012 19:34, Mr Javier Urriola Yaksic <javier.urriola at uq.net.au> 
wrote:
Dear MRtrix community,

Hi, during the data preprocessing I've corrected head motion and eddy current 
distortions by using eddy_current tool provided in FSL. However, so far I 
haven't  been able to rotate and adjust the b-matrix values in order to 
continue with the MRtrix diffusion processing.
How can I correct my b-values after eddy_correct registration?

Thanks in advance,

Javier
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-- 
Dr Jacques-Donald Tournier
Research Fellow
The Florey Institute of Neuroscience and Mental HealthMelbourne Brain Centre - 
Austin Campus245 Burgundy StreetHeidelberg  Vic  3084Ph:  +61 3 9035 7033Fax:  
+61 3 9035 7307www.florey.edu.au