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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 Venkateswaran,<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'>The outlier rejection is still
work-in-progress. We are about to post Version 3, in which there will be only
one threshold to simplify the function. Meanwhile please use very large numbers
for all thresholds to avoid the software to reject any images. <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'>However, there are two very handy
functions in “verify the results” section of the window, which are
two checkboxes with “create images of ,,,,”.<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'>After the calculation, please click the “Original-ADC-Mean-STD”
button. In this window, you can see your raw data and “theory image”,
which tells how the image should look like calculated from all data, and “error
image”, which is the difference between the raw and theory data. These
images can be very informative to detect corrupted images, typically observed
around the forth ventricle (brainstem, cerebellum, and often up to the splenium
of the corpus callosum). For the corrupted images, you can simply click the bad
image and large red X mark appears. These images won’t be included for
tensor calculation. <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'>In our experience, maybe well more than
50% of DTI data do not have significantly corrupted images and you don’t
need to worry. There are, however, sometimes subjects who have several corrupted
images. Once affected, it is common to see multiple severely corrupted ones. My
experience says pediatric brains are more prone to the artifacts. There are
sometimes signal leak from outside MRI that causes a spike in the k-space and
produce “zebra” patterns. This should also be eliminated. <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'>The “error images” also
sensitively detect subject motions and eddy current issues. These problems
appear as a ring around the brain. If the subject moved in the middle of the
scan, half the error images show bright edge in one side of the brain and dark
edge in the other side. The rest of the images have the same edges but with the
opposite bright/dark edge locations.<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'>You can try different threshold levels to
see if the software can automatically detect the one you thought bad. The
version 3 has better automatic detection, but these functions are still beta.<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'>Hope this helps.<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>
<div>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
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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>Rajagopalan, Venkateswaran<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, September 05, 2008
12:50 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] tensor
calculation - automatic outlier rejection</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'>Dear All,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'>Recently i downloaded latest version of
DTI studio. When i tried to do Tensor calculation the usual DTI- map options
appear first and when fill in the details and say ok another window pops up
asking for outlier rejection and when i say yes another window pops up where
there are many options to fill in. It will be of great help to me
if anyone could please tell me what this new automatic outlier
rejection option is for and where i can get details regarding how to choose
these different options and under what circumstances should i go for
this as i couldn't find their details in the manual.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'>Thanks<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:black'>venkateswaran<o:p></o:p></span></font></p>
</div>
</div>
<pre wrap><font size=2 face="Courier New"><span style='font-size:10.0pt'>===================================<o:p></o:p></span></font></pre>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=5 color=green face=Webdings><span style='font-size:18.0pt;font-family:
Webdings;color:green'>P</span></font><font size=2 color=navy face=Calibri><span
style='font-size:10.0pt;font-family:Calibri;color:navy'> </span></font><font
size=1 color=green face=Arial><span style='font-size:7.0pt;font-family:Arial;
color:green'>Please consider the environment before printing this e-mail</span></font><u1:p></u1:p><o:p></o:p></p>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Cleveland Clinic is ranked one of the top hospitals<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>in <st1:country-region
w:st="on"><st1:place w:st="on">America</st1:place></st1:country-region> by U.S. News & World Report (2008). <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Visit us online at http://www.clevelandclinic.org for<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>a complete listing of our services, staff and<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>locations.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Confidentiality Note: This message is intended for use<o:p></o:p></span></font></pre><pre><font
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size=2 face="Courier New"><span style='font-size:10.0pt'>and may contain information that is privileged,<o:p></o:p></span></font></pre><pre><font
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size=2 face="Courier New"><span style='font-size:10.0pt'>its entirety, whether electronic or hard copy. Thank you.<o:p></o:p></span></font></pre></div>
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