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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Alexi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thank you for the posting. You are right.
It seems that AIR made the registration worse. This is how the STD images and
image inspection window should be used; to check the registration quality as
well as image quality. If you have multiple repetition data, you can calculate
the STD image (actually subtracted image if you have only two repetitions). Misregistration
would show up as a ring around the brain as you found. If you don't have
repetition, you can also calculate discrepancies between fitted
(back-calculated from tensor fitting results) and raw DWIs. These images can be
obtained by choosing "Outlier Rejection = yes" when you do tensor
calculation and activate "create images of DWI-fitting from the estimated
tensor" and "create images of the difference between DWI-fitting and
original" boxes. The outlier rejection algorithm itself is still not
working perfectly (better version is coming out soon), but the "discrepancy"
images (raw minus fitted images) are handy to detect misregistration, eddy
current, and image corruption.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Now, your question is, why AIR made
registration worse. I don't have a definite answer, but the most probable
reason is the wrong threshold value. Unfortunately AIR is very sensitive to the
threshold value (the default is 50). The threshold is used to erase the noise
floor and avoid AIR to try to match noises. In my experience AIR tends to work
better with higher thresholds. The value 50 usually works for Philips scanner,
but Siemens tends to have much higher values. So, 150-250 seem to work better
(I don't know which scanner you are using). If you get poor results with AIR,
the first thing I recommend is to try higher threshold values. Once you get a
right value, usually you don't have to change it unless you have a major
upgrade or switch the scanner manufacture.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Please try it and let us know the results.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Susumu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Alexi Klimenko<br>
<b><span style='font-weight:bold'>Sent:</span></b> Saturday, March 15, 2008
2:56 PM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users] DTI
Studio</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Everyone, <br>
</span></font><font face="Courier New"><span style='font-family:"Courier New"'><br>
</span></font><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>I have a question about Dtistudio and image
registration.<br>
In the attached file you can find two standard deviations <br>
images, one of them is processed with AIR. <br>
<br>
I am leaning towards choosing the first series (stdA top row) as the <br>
second one show consistent ring-type intensities. Which one is suitable<br>
for further processing? <br>
<br>
To my suprise, however, stdB bottow row, is the one processed with<br>
AIR. Thank you. <br>
<br>
Alexi</span></font><o:p></o:p></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
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style='font-weight:bold'>Yahoo! Canada Messenger for the Web BETA</span></b></a><o:p></o:p></span></font></p>
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