<div dir="ltr">Thank you Dr. Mori. Your explanation was very helpful.<div><br></div><div>About DWI intensities, I am still perplexed to why the same subject gets so different DWI intensities, only 5 minutes apart. There must be something to do with the machine, all else being equal.</div>
<div class="gmail_extra"><br></div><div class="gmail_extra">Best regards.<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">I think it's happens. This is an expected range. Unless you turn off auto-gain setting in the second run, the scanner does automatic gain setting (something like automated determination of the volume of your stereo) and the signal intensity (equivalent of the loudness of the sound) varies.<div>
If you combine these two, the first scan with higher intensities receive more weighting (when both scans have corresponding b0s). If one of the scans lacks b0, then you have a problem.</div><div>I thought Hangyi once tried to implement cross-scan intensity normalization, but not sure if it is a default setup of the current version.</div>
<div>In your case, however, because you combine the two scans as one set, this type of cross-scan intensity normalization won't work. So you definitely have a problem by combining the two scans.</div></div><div>
<div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Fri, Sep 27, 2013 at 4:06 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"><div>Average DWI for the arcuate fibers, extracted from</div><div><br></div>Session 1 alone<div>mean DWI = 42.8095</div><div>mean b0 = 85.4266<br></div><div>FA= 0.5014</div><div><br><div><br></div><div>Session 2 alone</div>
<div>mean DWI = 54.6673<br></div></div><div>mean b0 = 109.7234<br></div><div>FA = 0.4830</div><div><br></div><div><br></div><div>Is it abnormal to have these differences between DTI runs? They were acquired one after the other, no other MRI sequence in between.</div>
<div><br></div><div><br></div><div><br></div><div>P.s. Calculations are from a subject that has both sessions complete, no b0 missing.</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">Then I believe the two sets have intensity differences by 10-20%.<div>Create the sum of all DWIs from the two scans and compare the intensity.</div>
</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Sep 27, 2013 at 3:27 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">MD seem to go down for the partial dataset:<br><div><br></div><div>Trace:</div><div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">2 DTI runs (normal) = 2.528e-003</div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">
2 DTI runs (exclude 1 b0) = 2.061e-003</div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">1 DTI run (normal) = 2.493e-003</div></div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">
<br></div><div style="font-family:arial,sans-serif;font-size:12.727272033691406px">Same ROIs were used to extract the fasciculus in each case.</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">how about MD?<div>Maybe intensities of two scans were different.</div></div><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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