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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'>oooops, I'll talk with Hangyi tomorrow and
clarify the issue. Maybe we should provide both methods.<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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</span></font></div>
<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>Hui Jing Yu<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, December 03, 2008
5:10 PM<br>
<b><span style='font-weight:bold'>To:</span></b> 'DTI Studio, ROI Editor,
Landmarker Questions/Support'<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
ImgVal Calculation</span></font><font size=3 face="Times New Roman"><span
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;color:#1F497D'>Hi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;color:#1F497D'>I received the following response from
Hangyi before (I believe he agrees with Jun Yi) that the statistical
calculation is normalized or weighted by fiber count.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'>-----Original
Message-----<br>
From: Hangyi Jiang [mailto:hjiang@jhmi.edu] <br>
Sent: Monday, November 24, 2008 1:20 PM<br>
To: hjyu@ic.sunysb.edu<br>
Subject: Re: [Mristudio-users] ImgVal Calculation<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'>hi,
<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'>this
kind of statistics in DTI Studio is based the fibers, not the pixels. for
example, if there are three fibers passing through a voxel, the image intensity
of this voxel will be counted three times when we calcualte the average image
intensity along the fibers. that is why we named them as
"Statistics ALONG THE FIBERS", not "..along the VOXELS that have
fibers".<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'>regards,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face=Consolas><span style='font-size:10.5pt'>Hangyi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;color:#1F497D'><o:p> </o:p></span></font></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<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>susumu<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, December 03, 2008
5:07 PM<br>
<b><span style='font-weight:bold'>To:</span></b> 'DTI Studio, ROI Editor,
Landmarker Questions/Support'<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
ImgVal Calculation<o:p></o:p></span></font></p>
</div>
</div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'><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'>Good question. No matter how many
reconstructed streamlines go through a pixel (1 or 10), the pixel is
"1". It is a binary operation. It would be interesting to try
normalized-line-number-weighted map, but DtiStudio doesn't do it.<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;font-family:"Times New Roman"'>
<hr size=2 width="100%" align=center>
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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>Jun Yi Wang<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, December 03, 2008
5:01 PM<br>
<b><span style='font-weight:bold'>To:</span></b> DTI Studio, ROI Editor,
Landmarker Questions/Support<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
ImgVal Calculation</span></font><font size=3 face="Times New Roman"><span
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>Hi
Dr. Mori,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>I
have a question to your response. The fiber density (fiber count/voxel)
is usually more than 1, so many line propagations or fibers will go through the
same voxels. When DTI Studio calculates mean FA for a reconstructed fiber
tract, does it calculate based on all voxels in the fiber tract with each voxel appear
once or based on fibers so that voxels belong to multiple fibers will be
appear multiple times?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>Thanks,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>Jun
Yi<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
<hr size=1 width="100%" align=center>
</span></font></div>
<p class=MsoNormal style='margin-bottom:12.0pt'><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'> susumu
<<st1:PersonName w:st="on">susumu@mri.jhu.edu</st1:PersonName>><br>
<b><span style='font-weight:bold'>To:</span></b> "DTI Studio, ROI Editor,
Landmarker Questions/Support" <mristudio-users@mristudio.org><br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday, December 3, 2008
3:36:46 PM<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
ImgVal Calculation</span></font><font size=3 face="Times New Roman"><span
style='font-size:12.0pt;font-family:"Times New Roman"'><o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>This is an interesting observation. It
should be a simple binary masking. The pixel with fibers are 1 and other pixels
are 0. We multiply this masking to loaded images and calculate average and STD.
Do you think our values are off? If so, this is definitely something we should
look into. Could you send us (not by MailingList) one fiber file and a co-registered
FA map?</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<div>
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face="Times New Roman"><span style='font-size:12.0pt;font-family:"Times New Roman"'>
<hr size=2 width="100%" align=center>
</span></font></div>
<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>Hui Jing Yu<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, November 21, 2008
1:56 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] ImgVal
Calculation</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>Dear
DTI Studio users,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>I
have a question regarding the ImgVal calculation under statistical profile for
fiber tracking. I got very different mean FA values (differences ranging
from 0.04 to 0.1) when I tried these two methods (keeping all parameters consistent
and same version of DTI):<o:p></o:p></span></font></p>
<p class=msolistparagraph><font size=2 face=Calibri><span style='font-size:
11.0pt'>1.</span></font><font size=1 face="Times New Roman"><span
style='font-size:7.0pt;font-family:"Times New Roman"'>
</span></font>Load previously saved fiber track (binary) into DTI studio, click
on fiber statistics and I have for Mean of ImgVal and Std. of ImgVal<o:p></o:p></p>
<p class=msolistparagraph><font size=2 face=Calibri><span style='font-size:
11.0pt'>2.</span></font><font size=1 face="Times New Roman"><span
style='font-size:7.0pt;font-family:"Times New Roman"'>
</span></font>Using MATLAB, apply the same binary fiber track onto FA image (analyze
format), calculate mean/std values for all the pixels/voxels belonging to this
fiber track<o:p></o:p></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>How
are these mean ImgVal calculated? I assume it is just a mean values for
all the pixels/voxels that are contained in the fiber track of interest.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>Thanks
in advance for your help.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Calibri><span style='font-size:11.0pt'>HJ<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:
12.0pt;font-family:"Times New Roman"'><o:p> </o:p></span></font></p>
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