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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Dear Dr. Mori<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks a lot for the guidance. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Because I am interested in doing further analysis like curvature
and torsion on the fiber bundles[1], I am curious about how DtiStudio bundle
fibers together. And I found that in the saved fiber tracking results from
DtiStudio with the option of Fiber Color as Random, it already assign fibers
with RGB colors. Does each bundle assign with unique combination of RGB colors?
I am wondering if there is an algorithm that DTIstudio uses to bundle
similar fibers together, like the one listed in the following paper. and
if the color is the only way to differentiate different bundles?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal style='background:white'><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'>[1] <a
href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Ding%20Z%22%5BAuthor%5D"><span
style='color:#1F497D;text-decoration:none'>Ding Z</span></a>, <a
href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Gore%20JC%22%5BAuthor%5D"><span
style='color:#1F497D;text-decoration:none'>Gore JC</span></a>, <a
href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Anderson%20AW%22%5BAuthor%5D"><span
style='color:#1F497D;text-decoration:none'>Anderson AW</span></a>. "Classification
and quantification of neuronal fiber pathways using diffusion tensor MRI".
<a href="javascript:AL_get(this,%20'jour',%20'Magn%20Reson%20Med.');"
title="Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine."><span
style='color:#1F497D;text-decoration:none'>Magn Reson Med.</span></a> 2003
Apr;49(4):716-21.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Sincerely,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Aifeng<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<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 mori<br>
<b>Sent:</b> Thursday, June 17, 2010 7:16 AM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] Saving fiber in data file<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>you can assign a color for each
bundle that share the same ROI.<br>
<br>
For example, you can first choose "red" and draw first ROI. Then all
reconstructed streamlines are painted red. Then choose "yellow" and
"AND+" tool. Draw another ROI for a portion of the reconstructed
streamlines. Those lines penetrates the second ROI becomes yellow while the
other lines stay red.<br>
<br>
You can save this results and the file format is explained in FAQ#1 in <a
href="http://www.mristudio.org">www.mristudio.org</a>.<br>
<br>
Another way is to reconstruct whatever the tracts you want in red and save it.
You can reconstruct the second tract independently using yellow and save it.<br>
<br>
After all the reconstructions are done and saved, you can load them back to
DtiStudio. In this way, you can show multiple tracts with different colors.<br>
<br>
Susumu<o:p></o:p></p>
<div>
<p class=MsoNormal>On Wed, Jun 16, 2010 at 10:49 PM, Zhang, Aifeng <<a
href="mailto:azhang@psych.uic.edu">azhang@psych.uic.edu</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal>Dr. Mori<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Does each fiber bundle has an unique RGB FiberColor? Is it
the way to identify fiber bundles? <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>and also where can I find the description about
the method of grouping fiber bundles? Thanks!<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Sincerely,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Aifeng<o:p></o:p></p>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'>
<hr size=2 width="100%" align=center>
</div>
</div>
<div>
<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"'> <a
href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>
[<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank">mristudio-users-bounces@mristudio.org</a>]
On Behalf Of susumu mori [<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>]<br>
<b>Sent:</b> Tuesday, June 15, 2010 7:30 PM<br>
<b>To:</b> DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
<b>Subject:</b> Re: [Mristudio-users] Saving fiber in data file</span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'>I hope FAQ#1 (<a
href="https://www.mristudio.org/wiki/faq" target="_blank">https://www.mristudio.org/wiki/faq</a>)
answers the question.<br>
<br>
susumu<o:p></o:p></p>
<div>
<p class=MsoNormal>On Tue, Jun 15, 2010 at 7:33 PM, Zhang, Aifeng <<a
href="mailto:azhang@psych.uic.edu" target="_blank">azhang@psych.uic.edu</a>>
wrote:<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear
DtiStudio,<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I
am trying to save the fiber tracking results into data file for further
analysis. The binary file lost the fiber direction information. I
am wondering if DtiStudio format keeps the coordinates and direction info for
each single fiber. If so, where can I locate the structure of the
DtiStudio format? thanks.<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely!<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Aifeng<o:p></o:p></p>
</div>
</div>
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