<div dir="ltr">how about MD?<div>Maybe intensities of two scans were different.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Sep 27, 2013 at 2:56 PM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Dr. Mori<div><br>That was my strategy. I combined the two runs, b0+32DWI+32DWI. This was done of course after registration, so that I could use the new gradient table. Images were saved in raw format, and loaded back with the new gradient table.</div>
<div><br></div><div>I tried both using all images with gradient 100, 100, 100 for the bad b0 or completely deleting the bad b0 (and the corresponding gradient line). Either way FA goes up a lot for the same measured tract. </div>
<div><br></div><div>Here are some more tests on left arcuate from a good subject with 2 DTI runs. Values are FA:</div><div>2 DTI runs (normal) = 0.489</div><div>2 DTI runs (exclude 1 b0) = 0.55</div><div>1 DTI run (normal) = 0.499</div>
<div><br></div><div>It seems that excluding one b0 is much worse than excluding the whole DTI run. In other words, adding DWI images from a sequence that doesn't have its own b0 may invalidate the findings. If seems that a set of DWI images without a b0 acquired during the same sequence is not useful to to include in DTI calculation.</div>
<div><br></div><div>Does this make sense?</div><div><br></div><div>Dorian</div><div><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/9/27 Susumu Mori <span dir="ltr"><<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Do you mean, you used different gradient tables for different runs?<div>I wonder if the gradient table and images are not matched for a part of data.</div>
<div>Suppose you have 1 b0 + 12 DWIs x 2 runs and you lost one b0 in the second run.</div>
<div>The only way to analyze this data, I can think of, is, combine the two runs as 1 b0 + 12 DWIs + 12 DWIs and crate one 25-element gradient table.</div><div><br></div><div>In general, if you have less data, you have lower SNR and FA goes up but I doubt if the loss of one b0 could cause such a large FA increase.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Fri, Sep 27, 2013 at 10:38 AM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Dear developers and Dr. Mori,<div><br></div><div>I am comparing FA for some tracts at two time points. At each time point I acquire 2-3 DTI runs to increase SNR. However, the scanner has malfunctioned for one of the runs in one subject. As a result the B0 image is not saved, but all other DWIs are there. So, I set the collapsed B0 to gradient 100, 100, 100 and align all DWIs to the only B0 available. For some results, the resulting FA is increased a lot.</div>
<div><br></div><div>I tried the same procedure with another subject, when I set one of the B0 to gradient 100, 100, 100, the resulting FA of the tract goes up from 0.51 to 0.62.</div><div><br></div><div>Is there any explanation why this is happening, and whether I should delete completely the collapsed B0 instead of setting it to 100, 100, 100?</div>
<div><br></div><div>Thank you.</div><div>Dorian</div><div>TJU</div></div>
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