Hi Julie,<br><br>Those are all good questions. Our TheoryAIR routine is now being updated to provide more controls over which transformation you want to use (currently Rigid only) and how to combine with outlier rejection (slice rejection or pixel rejection?). Also, currently you can't save TheoryAIRed data. I hope that we can release the revised version in this front in July.<br>
<br>As for the iteration, we are still accumulating experiences and want to welcome any information from users. At this point, I would say 5 usually works. DtiStudio provides visual interface to judge the improvement in registration. This is an effective method especially when you have repeated measurements (so that you can see the subtraction of the two to check the registration/correction quality). At this point, you should rely on your visual judgment.<br>
<br>As a matter of fact, almost always, difficulty of automated image quality check is how to quantify the improvement by registration/correction schemes. If you can quantify the improvement, we would use such a measure to minimize during the registration and correction process. In the end, our eyeballs are the best method for judgment which we can hardly beat.<br>
<br><br>Susumu<br><br><div class="gmail_quote">On Thu, Jun 17, 2010 at 7:27 PM, Julie McEntee <span dir="ltr"><<a href="mailto:jmcentee@jhmi.edu">jmcentee@jhmi.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>
<font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;">Hi Susumu,<br>
<br>
I was wondering if you have been able to follow-up on your points in the email to Darren (below).<br>
<br>
I read the response re: TheoryAir from Hangyi, but it did not indicate whether TheoryAir does a regid or affine transform to answer whether or not it would be able to do eddy current correction-?<br>
<br>
I am able to do the Pixel rejection using Darren’s method and obtain results with binary mask & no “Image rejection”; however, I get Image rejection after performing TheoryAir- is that expected? How do you determine the # of iterations to perform with TheoryAir?<br>
<br>
Lastly, if I want to do TheoryAir and Pixel rejection, would I do TheoryAir, save DWI + b0 images as REC file, re-load into DtiStudio, and then perform Pixel rejection/tensor calculation?<br>
<br>
Thanks for your help,<br>
<br>
Julie<br>
<br>
Julie E. McEntee, MA, CCRP<br>
Senior Research Program Coordinator<br>
Department of Psychiatry- Neuroimaging<br>
Johns Hopkins University School of Medicine<br>
600 N. Wolfe St./Phipps 300<br>
Baltimore, MD 21287<br>
Phone: 410-502-0468<br>
Fax: 410-614-3676<div class="im"><br>
<br>
<br>
On 5/18/10 10:48 AM, "susumu mori" <<a href="http://susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>> wrote:<br>
<br>
</div></span></font><blockquote><div class="im"><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;">Darren,<br>
<br>
You are using the "Pixel rejection" correctly and we have to investigate why you are getting "Image rejection" results.<br>
<br>
<br>
</span></font><blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;">1) Should I run other registration methods such as AIR or MI before<br>
theory-registratin? Will theory-registration take care of eddy current<br>
correction?<br>
</span></font></blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;"><br>
>Theory registration should be used instead of AIR or MI. I have to confirm Hangyi if TheoryAIR does rigid or affine. I'll get back to you with this respect too.<br>
<br>
</span></font><blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;"><br>
2) What images are changed by theory registration? The original<br>
images? It doesn't seem to produce new images such as with mutual<br>
information or AIR.<br>
</span></font></blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;"><br>
>Yes, when you use TheoryAIR, you don't get a copy. The original images are overwritten.<br>
<br>
</span></font></div><blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt;"><div class="im"><br>
Thanks,<br>
Darren<br>
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