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<div class="moz-cite-prefix">Hello<br>
<br>
I confirm too (here is the explanation from the fsl list)<br>
<br>
<pre wrap="">The -nosearch is to stop an <b class="moz-txt-star"><span class="moz-txt-tag">*</span>extensive<span class="moz-txt-tag">*</span></b> 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.
</pre>
(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)<br>
<br>
<br>
And to answer the first question of Javier you can use the fsl
script (fdt_rotate_bvec) that you can find there :<br>
<a class="moz-txt-link-freetext"
href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;3777d8fe.1202">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;3777d8fe.1202</a><br>
(NOte that this does not correct for the bvalue but for the
direction (bvecs) )<br>
<br>
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.<br>
<br>
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)<br>
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 ...<br>
<br>
cheers<br>
<br>
Romain<br>
<br>
<br>
<br>
Le 04/09/2012 15:43, Matteo Figini a écrit :<br>
</div>
<blockquote
cite="mid:21807454.11645141346766191873.JavaMail.root@wmail46"
type="cite">
<pre wrap="">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: <a class="moz-txt-link-abbreviated" href="mailto:d.tournier@brain.org.au">d.tournier@brain.org.au</a>
Data: 04/09/2012 2.27
A: "Mr Javier Urriola Yaksic"<a class="moz-txt-link-rfc2396E" href="mailto:javier.urriola@uq.net.au"><javier.urriola@uq.net.au></a>
Cc: <a class="moz-txt-link-rfc2396E" href="mailto:mrtrix-discussion@www.nitrc.org">"mrtrix-discussion@www.nitrc.org"</a><a class="moz-txt-link-rfc2396E" href="mailto:mrtrix-discussion@public.nitrc.org"><mrtrix-discussion@public.nitrc.org></a>
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 <a class="moz-txt-link-rfc2396E" href="mailto:javier.urriola@uq.net.au"><javier.urriola@uq.net.au></a>
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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</pre>
</blockquote>
<br>
<br>
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