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<div style="DIRECTION: ltr" id="divRpF275258">Thanks for the comprehensive reply.</div>
<div style="DIRECTION: ltr"><font size="2" face="tahoma">Yes, your assumption of what I meant - the mean streamline - is correct.</font></div>
<div style="DIRECTION: ltr"><font size="2" face="tahoma">The weighted FA calculation would be useful, thanks Hangyi.</font></div>
<div style="DIRECTION: ltr"><font size="2" face="tahoma"></font> </div>
<div style="DIRECTION: ltr"><font size="2" face="tahoma">many thanks</font></div>
<div style="DIRECTION: ltr"><font size="2" face="tahoma">Linda</font></div>
<div style="DIRECTION: ltr"> </div>
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<font color="#000000" size="2" face="Tahoma"><b>From:</b> mristudio-users-bounces@mristudio.org [mristudio-users-bounces@mristudio.org] On Behalf Of susumu mori [susumu@mri.jhu.edu]<br>
<b>Sent:</b> July 15, 2011 9:09 PM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support; Hangyi Jiang<br>
<b>Subject:</b> Re: [Mristudio-users] Mean FA<br>
</font><br>
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<div>Hi Linda,
<div><br>
</div>
<div>I'm not sure what you exactly mean by "mean tract position". To calculate a mean, you need a population. The "population" could be across 10 different individuals, 10 repeated scans, 10 voxels within the same individual, etc. </div>
<div><br>
</div>
<div>I assume that you meant; "after tractography, it is common to obtain 10s of streamlines that belong to the same pathway and can we calculate a "mean streamline" of the 10s of streamlines?"</div>
<div><br>
</div>
<div>If so, DtiStudio doesn't have such a function explicitly, but has the following functions;</div>
<div><br>
</div>
<div>1) After tractography (and thus obtained 10s of streamlines), this information is converted to 1/0 binary masking, in which voxels that contain the streamline are assigned "1". Then it reports mean FA of the masked voxels.</div>
<div>2) In the above method, a voxel that contains 1 streamline and 10 streamlines are both equally weighted (they are both assigned "1"). I believe that there is a function to perform "weighted FA calculation". Please ask Hangyi about the detail of this function.
This may provide a similar result to calculating a mean tract and measuring FA.</div>
<div><br>
</div>
<div>To divide the tractography results, DtiStudio can report FA of a tract at each slice level. For example, if you have 50 axial slices, you can get a report of FA at 50 axial levels. Then the problem is, you have to identify corresponding axial levels when
you compare the reported slice-specific numbers across individuals. For example, the FA of the CST at axial slice #24 may correspond to slice #26 of another subject. When you get FA of the entire CST from the pons to the motor cortex, you don't have this problem.
As soon as dividing the CST into "regions", you need spatial normalization across individuals to make sure you are comparing the same "regions" across individuals. </div>
<div><br>
</div>
<div>There are several ways to do this normalization. Probably the easiest way is to normalize the orientation and the size of the brains across the population using a linear transformation such that each axial level is more or less consistent and thus the
slice-by-slice reporting can be population averaged. Or you can use our full brain segmentation using the DiffeoMap/RoiEditor pipeline such that the CST pathway can be divided into anatomical segments such as "pons", "midbrain", "internal capusule", "corona
radiata".</div>
<div><br>
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<div>Hope this helps.<br>
<br>
<div class="gmail_quote">On Fri, Jul 15, 2011 at 6:14 PM, Linda Lanyon <span dir="ltr">
<<a href="mailto:llanyon@eyecarecentre.org">llanyon@eyecarecentre.org</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div lang="EL">
<div style="FONT-FAMILY: Tahoma; DIRECTION: ltr; COLOR: #000000; FONT-SIZE: 13px">
<div>Is there a way in DTI Studio (or MRI Studio) to find a mean tract position for a bundle of fibers along the same pathway, and then to calculate mean FA along that tract (preferably divided into segments along the tract)?</div>
<div><font size="2" face="tahoma"></font> </div>
<div><font size="2" face="tahoma"><font face="tahoma">The only method I can find in DTI Studio is to reduce the tracts down to a selected few and then perform statistics, which gives mean FA. - just wondering if there is a way to get the mean tract as I've
seen this published with other software.</font></font></div>
<div><font size="2" face="tahoma"></font> </div>
<div><font size="2" face="tahoma">Thanks!</font></div>
<div><font size="2" face="tahoma">Linda</font></div>
<div><font size="2" face="tahoma"></font> </div>
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<div><font size="2">
<div>------------------------------------------------------------------------------------------------<br>
Linda Lanyon PhD BSc(Hons) CEng CITP MBCS<br>
Michael Smith Foundation for Health Research Post Doctoral Research Fellow<br>
University of British Columbia, Human Vision & Eye Movement Laboratory<br>
VGH Eye Care Centre, 3rd Floor Research Labs <br>
2550 Willow St, Vancouver<br>
Phone: <a href="tel:%2B1-604-675-8865" target="_blank" value="+16046758865">+1-604-675-8865</a><br>
Cell: <a href="tel:%2B1-778-378-5545" target="_blank" value="+17783785545">+1-778-378-5545</a><br>
Fax: <a href="tel:%2B1%20604-875-4663" target="_blank" value="+16048754663">+1 604-875-4663</a><br>
email: <a href="mailto:llanyon@eyecarecentre.org">llanyon@eyecarecentre.org</a><br>
web: <a href="http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm" target="_blank">
http://www.neuroophthalmology.ca/UBCNeuroOp/JBarton/labstaff/Linda.htm</a><br>
<font size="2"><br>
Director, Society for Canadian Women in Science and Technology: <a href="http://www.scwist.ca" target="_blank">
www.scwist.ca</a><br>
<em>SCWIST is a non-profit association that promotes, encourages and empowers women<br>
and girls in science, engineering and technology.<br>
</em></font><font size="2">------------------------------------------------------------------------------------------------</font>
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<div>"If we knew what it was we were doing, it would not be called research, would it?"<br>
Albert Einstein</div>
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