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<p class=MsoNormal><span style='color:#1F497D'>Hi,<o:p></o:p></span></p>
<p class=MsoNormal><span style='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></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoPlainText>-----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></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>hi, <o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>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></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>regards,<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Hangyi<o:p></o:p></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b>On Behalf Of </b>susumu<br>
<b>Sent:</b> Wednesday, December 03, 2008 5:07 PM<br>
<b>To:</b> 'DTI Studio, ROI Editor, Landmarker Questions/Support'<br>
<b>Subject:</b> Re: [Mristudio-users] ImgVal Calculation<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:navy'><o:p> </o:p></span></p>
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<hr size=2 width="100%" align=center>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
mristudio-users-bounces@mristudio.org [mailto:mristudio-users-bounces@mristudio.org]
<b>On Behalf Of </b>Jun Yi Wang<br>
<b>Sent:</b> Wednesday, December 03, 2008 5:01 PM<br>
<b>To:</b> DTI Studio, ROI Editor, Landmarker Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] ImgVal Calculation</span><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>Hi Dr. Mori,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>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></p>
</div>
<div>
<p class=MsoNormal>Thanks,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Jun Yi<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><b><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> susumu <susumu@mri.jhu.edu><br>
<b>To:</b> "DTI Studio, ROI Editor, Landmarker Questions/Support"
<mristudio-users@mristudio.org><br>
<b>Sent:</b> Wednesday, December 3, 2008 3:36:46 PM<br>
<b>Subject:</b> Re: [Mristudio-users] ImgVal Calculation</span><span
style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p>
<div>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
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><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:navy'> </span><o:p></o:p></p>
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<hr size=2 width="100%" align=center>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b>On Behalf Of </b>Hui Jing Yu<br>
<b>Sent:</b> Friday, November 21, 2008 1:56 PM<br>
<b>To:</b> mristudio-users@mristudio.org<br>
<b>Subject:</b> [Mristudio-users] ImgVal Calculation</span><o:p></o:p></p>
</div>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>Dear DTI Studio users,<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>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></p>
<p class=MsoListParagraph>1.<span style='font-size:7.0pt;font-family:"Times New Roman","serif"'>
</span>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>2.<span style='font-size:7.0pt;font-family:"Times New Roman","serif"'>
</span>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>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></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>Thanks in advance for your help.<o:p></o:p></p>
<p class=MsoNormal> <o:p></o:p></p>
<p class=MsoNormal>HJ<o:p></o:p></p>
</div>
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<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p>
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