Hi Donald, <div><br></div><div>Thank you for addressing my question. It makes perfect sense to color the FOD according to the xyz coordinates. My initial question actually mainly concerns the symmetry of colors to the center of FOD. As I looked closely later at the FOD profiles that MRtrix generated, they were actually symmetric to the center. So there is no question for that now. Sorry for my earlier misunderstanding. </div>
<div><br></div><div>The region of my interest contains crossing fibers from approximately both y (green) and z (blue) directions. If these two different colors were mixing in the same lobes of FOD instead of being separated in different lobes (as you saw from the example i sent), does it indicate that the FOD didn't resolve those fibers from two different directions? In this case, is there still any chance for the fiber tracking algorithm to resolve them in those voxels? Please let me know if this question is clear. <br>
<br></div><div>Thanks, </div><div>Zhuang</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Tue, Mar 12, 2013 at 5:25 PM, Donald Tournier <span dir="ltr"><<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Zhuang,<div><br></div><div>The colour-coding is done strictly according to the X,Y,Z components at that point on the surface, with no regard to which FOD lobe that point might visually appear to belong to. You'll find the full width at half-max of the FOD peaks at lmax 8 are around ~20°, so for an off-axis peak like the one you're showing, the actual peak might be along Z-Y (giving a greenish-blue colour - cyan), but one side of the lobe might be closer to Z (blue) and the other closer to Y (green). </div>
<div><br></div><div>Colour-coding according to the closest peak direction could be done, and might be OK when the peaks are well-defined, but there will definitely be cases when two peaks are close to each other and aren't resolved properly, in which case this approach would give misleading results. The current approach is unambiguous and easy to implement, and as far as I know, similar to what other packages might do. <br>
<br>Cheers,</div><div><br></div><div>Donald.<div><div class="h5"><br><br><br><div class="gmail_quote">On 13 March 2013 10:47, Zhuang Song <span dir="ltr"><<a href="mailto:zhuang.song@gmail.com" target="_blank">zhuang.song@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br><div>I am having some problem to understand the color coding of the FOD profile constructed by the CSD method of MRtrix. For my understanding, the color should be the same along the same axis of the FOD. However quite often I see the color changes a lot along the same orientation of FODs. </div>
<div><br></div><div>I attached one example picture of FOD here but not sure if you can see the attachment in this maillist. In this example, the FOD color changes from green to blue in the first primary orientation. What should I interpret it? Does it mean that the primary direction is a mix of diffusion in both green and blue directions? </div>
<div><br></div><div>Thanks, </div><span><font color="#888888"><div>Zhuang </div>
</font></span></blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div>
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