<div dir="ltr">HI Durai,<div><br></div><div style>Yes, if the brain rotates, the contrast changes and therefore simple rotation registration is, strictly speaking, not accurate.</div><div style>There are papers discussing this issue and we usually solve this by rotating the gradient vector together.</div>
<div style><br></div><div style>For example, we apply [1, 0, 0] gradient in the first image. In the second image, we apply the same direction but the brain was rotated. In the post-processing, we re-rotate the brain to register the second brain to the first brain. In this case, the gradient orientation of the second "re-rotate (registered)" image is no longer [1, 0, 0]. So we apply the rotation not only the image but also the gradient orientation.</div>
<div style><br></div><div style>In reality, typical DWI data should have rotation less than 1 degree within typical 5-10 min scans. So I expect this won't be a big issue, but if the brain does rotate more than 1 degree, the gradient re-orientation does make difference. However, if the subject moves 2-3 degree, these data are definitely outliers, which often suffer from slice-by-slice registration errors WITHIN one 3D volume (you can't correct it unless the rotation is purely within the 2D imaging plane) and signal dropout. So, the issue is usually not as simple as applying the gradient re-orientation and become a happy person.</div>
<div style><br></div><div style>We are working on a comprehensive QC report to deal with this issues. I think it will come out this year but you can have a working version in the latest DtiStudio. Hangyi, is it correct? Do we have Yue's QC reporting function already in DtiStudio?</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 24, 2013 at 1:44 AM, Durai Arasan <span dir="ltr"><<a href="mailto:durai23@gmail.com" target="_blank">durai23@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<div><br></div><div>A general question about motion correction in diffusion imaging. In fmri this is a commonly practiced preprocessing step where the new signal, say, F' is obtained by a spatial shift of F, signal acquired when movement occurred:</div>
<div><br></div><div>F' = F*m</div><div><br></div><div>where m = m(x,y,z), the motion matrix.</div><div><br></div><div>But in diffusion this is clearly not the case as the signal in each direction is a function not only of the position of the brain but also of individual brain geometry. Therefore, new signal D' will be a <u>transform</u> (not shift) of signal D, acquired when movement occurred:</div>
<div><br></div><div>D' = D*t</div><div><br></div><div>where t = t(x,y,z,brain_geometry), the transform factor. </div><div><br></div><div>So unless there is an estimate of t, I don't think any motion correction is going to be useful in diffusion, certainly not a simple rigid body adjustment. Am I wrong?</div>
<div><br></div><div>Thanks</div><span class="HOEnZb"><font color="#888888"><div>Durai</div><div><br></div><div><br></div>
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