<p dir="ltr">Hi Dorian,</p>
<p dir="ltr">Romain's pretty much covered all the bases already, but I just thought I'd throw in my 2 cents. In my experience corruption isn't really specific to any manufacturer, and is usually caused by subject motion. Either gross motion, which is often associated with slice dropout due to spin history effects, or pulsatile motion due to the cardiac cycle, particularly near the 4th ventricle in front of the cerebellum. The bed vibration problem is typically very reproducible, and causes problems in specific areas (mid-sag parietal in our case), so doesn't really fit with what you're describing. I've never personally had issues with gradient heating, so can't comment. I've also very occasionally seen slices just drop out completely for no apparent reason, which I can only attribute to some kind of hardware problem (RF issues maybe?).</p>
<p dir="ltr">As to the Romain's mention of a fix for this in the next release of MRtrix, I have to set the record straight: this is very much at the planning stage right now! I'll be working on it, but there's nothing at this point. Sorry...</p>
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: +44 (0)20 7188 7118 ext 53613<br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote">On 6 Nov 2013 14:54, "Dorian P." <<a href="mailto:alb.net@gmail.com">alb.net@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Romaine,<div><br></div><div>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.</div><div>Subject motion should also play a role, otherwise I don't explain why some subjects don't have bad slices.</div>
<div><br></div><div>The fourier transform is a new reason I never knew about. Is there a way to change fourier parameters in the scanner?</div><div><br></div><div>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.</div>
<div><br></div><div>Despite this, do you know when is the expected release of mrtrix with slice correction?</div><div><br></div><div>Thank you.</div><div><br></div><div>Dorian</div><div>TJU</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2013/11/6 romain valabregue <span dir="ltr"><<a href="mailto:romain.valabregue@upmc.fr" target="_blank">romain.valabregue@upmc.fr</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hello<br>
<br>
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<br>
_ subject motion (when there is a lot of subject motion then I see
several dropout on the same volume<br>
_ bed vibration a know problem on TRIO 3T (I heard they had a
solution but we could not convince them to install it ...)<br>
_ gradient heating<br>
_ 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."<br>
<pre></pre>
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)<br>
<br>
in the next mrtrix release there will be a correction for those
'bad' slice<br>
<br>
Cheers<br>
<br>
Romain<br>
<br>
Le 05/11/2013 15:13, Dorian P. a écrit :<br>
</div>
<blockquote type="cite"><div><div>
<div dir="ltr">Dear MRtrix list,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>My question at this point is:anybody had the same
experience with slice dropouts?</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Finally, do you think the slice collapse is related to the
anterior-posterior shift (gradient heating) problem?</div>
<div><br>
</div>
<div>Any comment may be useful.</div>
<div>Thank you.</div>
<div><br>
</div>
<div>Dorian</div>
<div>TJU</div>
</div>
<br>
<fieldset></fieldset>
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