Post edited 10:24 am – December 12, 2011 by Laura

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Hi,

I was trying to work with the resulting "_odf.nii" file with Matlab and realise that the values in each voxel aren't between 0-1 as expected.

I load the file considering that the ODF file is a 4 byte float numbers, as you mention in the webpage for file format information. The ranging values are:

% "load_nii .m" from http://www.mathworks.com/matla…..lyze-tools

>>ODF=load_nii('dsi_odf.nii');

>> max(max(max(max(ODF.img))))

ans =

   487500480

>> min(min(min(min(ODF.img))))

ans =

     0

 

Also, when I plot the ODF with the given "181_vecs.txt", in almost every voxel I tried, the ODF is oriented perpendicular to the maximum expected. That's why I guess that maybe, I am not reading correctly the values (don't take into account the x,y,z axis values).

% ODF in one voxel

% In blue: the expected direction orientation

% ODF values with red(max_value)-blue(min_value)

 

Is there something wrong? What is the meaning of the resulting values?

I want to obtain de ODF values as a distribution function, that is, between 0-1. (*)

Any suggestion?

 

 

Thanks in advance,

Laura

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* (ODF equation in page 36) Hagmann, Patric (April 21, 2005). "From Diffusion MRI to Brain Connectomics" (PDF). Ecole Polytechnique Federale de Lausanne. Ph.D. Thesis. pp. 1, 107.

I don't know exactly what happens with the orientation. I tried to plot a fibber from the corpus callosum, the ODFs and the expected direction, and they match. Therefore, no reorientation is needed.

But in some cases, even if there are no crossing fibers in the voxel, the ODF doesn't match with the expected direction. I guess I am doing something wrong.

 

I have another question. I don't understand the meaning of the ODF values.

The ODF computed for DSI and QBALL or HARDI is the same? I mean, ODF_qball doesn't take into account the solid angle (factor r^2) and DSI does?

I am working with DSI.

 

I know how to normalize anyway, but I would like to understand the meaning of this values.

Thanks in advance.