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

Fri Sep 7 02:03:31 PDT 2012

Hello

I confirm too (here is the explanation from the fsl list)

The -nosearch is to stop an*extensive*  initial search of rotation angles.
It does not the optimisation method from finding non-zero rotations, and
you will find that it does in fact correct for rotations.

(I guess it comes from the old time where one had to coregister a 
sagital T1 with an axial EPI both in analyze format which has no 
orientation information)

And to answer the first question of Javier you can use the fsl script 
(fdt_rotate_bvec) that you can find there :
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;3777d8fe.1202
(NOte that this does not correct for the bvalue but for the direction 
(bvecs) )

then you just need to convert the new bvec in mrtrix format using the 
tool of Luis Concha (he send yesterday) or the one in matlab I just send.

About higher B value I agree this is a tricky thing to get a good 
registration. I know that Jesper Andersson propose a new script that 
will been incorporate in the FSL 5 release (planned for next week)
There will be also a very interesting script (also from Jesper) that 
correct for EPI deformation using a B0 acquisition with an opposite 
phase direction. (it should work much better than with a field map). 
This script will also do the eddy current correction so may be it will 
be better for higher B value ... let's try it next week ...

cheers

Romain

Le 04/09/2012 15:43, Matteo Figini a écrit :
> 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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>

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