[Mrtrix-discussion] Re: color coding of FODs

[Zhuang Song]

Hi Donald,
Thanks for getting back to this. Your understanding of my question is
correct. I have just tried the fiber tracking with both deterministic and
probabilistic modes. Even though the FOD didn't resolve the crossing
fibers, probabilistic tracking was still able to track in both directions
in some of those voxels. It is great that you provide the probabilistic
tracking option.

Zhuang


On Sun, Mar 17, 2013 at 8:33 PM, Donald Tournier <d.tournier at brain.org.au>wrote:

> Hi Zhuang,
>
> I'm not sure I completely understand what you're asking. Are you saying
> you have a region of fibres running anterior-posterior (green) and some
> running inferior-superior (blue), and that in some voxels you get a single
> FOD peak with an intermediate orientation/colour? It might help if you
> could post an screenshot of the problem (use the MRView 'Orientation plot'
> sidebar tool, with the 'overlay' option). If did I understand correctly,
> then yes, this does mean that the fibre orientation were not resolved, and
> yes, this will influence the tracking results.
>
> Also, in general I wouldn't worry about the colours of the FOD, they're
> really only useful for display purposes. The *shape* of the FOD is what
> matters, and in your case, a single FOD peak/lobe when you were expecting 2
> distinct peaks tells you that the orientations have not been resolved.
>
> Hope that helps.
> Cheers,
>
> Donald.
>
>
> On 14 March 2013 11:07, Zhuang Song <zhuang.song at gmail.com> wrote:
>
>> Hi Donald,
>>
>> 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.
>>
>> 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.
>>
>> Thanks,
>> Zhuang
>>
>>
>>
>> On Tue, Mar 12, 2013 at 5:25 PM, Donald Tournier <d.tournier at brain.org.au
>> > wrote:
>>
>>> Hi Zhuang,
>>>
>>> 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).
>>>
>>> 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.
>>>
>>> Cheers,
>>>
>>> Donald.
>>>
>>>
>>>
>>> On 13 March 2013 10:47, Zhuang Song <zhuang.song at gmail.com> wrote:
>>>
>>>>
>>>> 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.
>>>>
>>>> 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?
>>>>
>>>> Thanks,
>>>> Zhuang
>>>>
>>>
>>>
>>>
>>> --
>>> *Dr Jacques-Donald Tournier
>>> *
>>> Research Fellow
>>>
>>> The Florey Institute of Neuroscience and Mental Health
>>> Melbourne Brain Centre - Austin Campus
>>> 245 Burgundy Street
>>> Heidelberg  Vic  3084
>>> Ph:  +61 3 9035 7033
>>> Fax:  +61 3 9035 7307
>>> www.florey.edu.au
>>>
>>>
>>
>
>
> --
> *Dr Jacques-Donald Tournier
> *
> Research Fellow
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg  Vic  3084
> Ph:  +61 3 9035 7033
> Fax:  +61 3 9035 7307
> www.florey.edu.au
>
>
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