[Mrtrix-discussion] Slice collapse problems

[Dorian P.]

Hi Romaine,

Our scanner is Philips Achieva 3T. Similar to your explanation, I was told
vibrations can be a cause, and I was pointed to a paper by Gallichan et al.
on HBM.
Subject motion should also play a role, otherwise I don't explain why some
subjects don't have bad slices.

The fourier transform is a new reason I never knew about. Is there a way to
change fourier parameters in the scanner?

It would be great to have mrtrix fix or remove bad slices. But... I think
this needs concurrent motion correction. In fact, if motion correction is
done in other software before bringing the data to mrtrix, bad slices will
contaminate nearby slices. At that point instead of having one bad slice we
would have two or more. I had this experience with regular DTI, where bad
slices I flagged before realignment were spread in adjacent slices making
them more blurry after ralignment.

Despite this, do you know when is the expected release of mrtrix with slice
correction?

Thank you.

Dorian
TJU


2013/11/6 romain valabregue <romain.valabregue at upmc.fr>

>  Hello
>
> Yes signal dropouts is a common feature of Siemens dti acquisition. but it
> is not clear what is the exact cause. I think there may be different cause
> _ subject motion (when there is a lot of subject motion then I see several
> dropout on the same volume
> _ bed vibration a know problem on TRIO 3T (I heard they had a solution but
> we could not convince them to install it ...)
> _ gradient heating
> _ partial fourier : Jesper on fsl list : " My personal experience is for
> example that 5/8 is to severe and that 3/4 is better for reducing drop-out."
>
> For the gradient heating you can try to increase the TR (take 1 or 2
> second abouve  the minimal TR ). The bvec order may also play a role : make
> sure you the directions where the absolute amplitude on a given axis (it is
> often the case)
>
> in the next mrtrix release there will be a correction for those 'bad' slice
>
> Cheers
>
> Romain
>
> Le 05/11/2013 15:13, Dorian P. a écrit :
>
> Dear MRtrix list,
>
>  My HARDI sequence is frequently contaminated by slices with collapsed
> signal. This happens in 2-3 slices of 61 volumes. Slices and volumes
> affected are a bit random, not always the same.
>
>  In concomitance I see shifts in anterior-posterior (phase) direction
> from one volume to the other. I have been told this may happen because
> gradients heat to much.
>
>  My question at this point is:anybody had the same experience with slice
> dropouts?
>
>  Do you think slice dropouts are related to the b-value. Would decreasing
> b from 3000 to 2500 make a difference? Could slices collapse because of
> motion causing bigger artifacts with high b-values?
>
>  Finally, do you think the slice collapse is related to the
> anterior-posterior shift (gradient heating) problem?
>
>  Any comment may be useful.
> Thank you.
>
>  Dorian
> TJU
>
>
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