[Mrtrix-discussion] Color and shape of the FODs or ODFs

Wed Apr 30 01:45:17 PDT 2014

Hi Rob,

that was really really helping. I find it really hard, if it comes to an exact and correct interpretation of results.

Thanks a lot,

Ralf

+++++++++++++++++++++++++++++++++++++++++++++++
Ralf Lützkendorf
Department for Biometry and Medical Informatics
University of Magdeburg, Germany
phone: +49 391 67 13546
fax: +49 391 67 13536

________________________________
Von: mrtrix-discussion-bounces at www.nitrc.org [mrtrix-discussion-bounces at www.nitrc.org]" im Auftrag von "Robert Smith [r.smith at brain.org.au]
Gesendet: Mittwoch, 30. April 2014 04:44
An: Thijs Dhollander
Cc: MRtrix discussion
Betreff: Re: [Mrtrix-discussion] Color and shape of the FODs or ODFs

Ralf

The apparent colour mismatch of the corresponding antipodal FOD lobes is a bit of an illusion. The lobes are not explicitly coloured based on the peak direction; rather, every vertex on the mesh is coloured according to its direction from the origin in order to render the surface. Then, because you are not looking precisely at the peaks of each lobe but rather the side of each lobe closest to the camera position, and each lobe has a finite angular width, you are in fact not looking at antipodal vertices; hence the apparent colour difference. Rest assured that if you looked precisely at the peak of each antipodal lobe, and disabled any lighting effects, the colours would be identical.

As far as interpreting the 'shape' of the FOD, I can think of three possible interpretations of the question:

  1.  Size: See this paper<http://www.ncbi.nlm.nih.gov/pubmed/22036682>, and stay tuned for further updates :-P
  2.  Number of discrete fibre populations: This one<http://www.ncbi.nlm.nih.gov/pubmed/22611035> is worth a look.
  3.  Parameterisation of the angular distribution of fibre orientations within discrete fibre populations: This is a bit trickier; mostly people try to incorporate e.g. measures of fibre orientation dispersion into their diffusion models, so it's no longer spherical deconvolution-based. Think this one<http://www.ncbi.nlm.nih.gov/pubmed/17596967> was the first, but don't quote me on that. Expect to see quite a bit on this over the next couple of years, as it has implications for tractography.

Cheers
Rob

--

Robert Smith, Ph.D
Research Officer, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au<http://www.florey.edu.au>

On Tue, Apr 29, 2014 at 5:47 PM, Thijs Dhollander <thijs.dhollander at gmail.com<mailto:thijs.dhollander at gmail.com>> wrote:
Hi Ralf,

The shape of the FOD is easy to interpret: you basically start with a (unit) sphere, and then scale its radius along each orientation by the FOD amplitude for that orientation.  It's basically the 3D version of polar coordinates ( http://en.wikipedia.org/wiki/Polar_coordinate_system ), but used to represent a 2D spherical function in a 3D space.
The RGB values for the colors are simply derived from a normalized vector that points along each direction.  The colors are nothing more than a visual aid though; they help you navigate a field of FODs much easier.

The caption in figure 7 refers you to the webversion, because the printed version probably did not feature colors at the time.  The word "interpretation" there, only means that whatever is written in the caption about colors, can only really be visually appreciated in the (colored) digital version.  The normal PDF at Elsevier basically is that web version. :-)

Hope this clarifies some things!

Cheers,
Thijs

Thijs Dhollander
thijs.dhollander at gmail.com<mailto:thijs.dhollander at gmail.com>
Tel. +32 475 36 44 27<tel:%2B32%20475%2036%2044%2027>
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven

On Mon, Apr 28, 2014 at 3:46 PM, Luetzkendorf, Ralf <Ralf.Luetzkendorf at med.ovgu.de<mailto:Ralf.Luetzkendorf at med.ovgu.de>> wrote:
Hello MRTrix Community,

I have a question about the color and shape of the FODs / ODFs
I read through the papers and I have to be absolutely sure how to interpret them.

At first in the Paper "Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution, 2004" Figure 7 referred you to a web version for color interpretation. Is there still a Web Version? I only found the normal PDF at Elsevier.

Do these drop-shaped geometrical bodies, that face each other have exactly the same color? And its only a rendering problem, that they very often don't have it in figures, like in Figure 7 of the 2004 Article?

Is there a description how to interpret the shape of the ODF /FOD. Something like a first and still established paper about it?

Thanks for the help,

Ralf

_______________________________________________
Mrtrix-discussion mailing list
Mrtrix-discussion at www.nitrc.org<mailto:Mrtrix-discussion at www.nitrc.org>
http://www.nitrc.org/mailman/listinfo/mrtrix-discussion

_______________________________________________
Mrtrix-discussion mailing list
Mrtrix-discussion at www.nitrc.org<mailto:Mrtrix-discussion at www.nitrc.org>
http://www.nitrc.org/mailman/listinfo/mrtrix-discussion