AFNI v.s. FSL

Sunday, October 2, 2011

AFNI v.s. FSL

http://neurohub.ecs.soton.ac.uk/index.php/Software:AFNI

DTI program: dtifit (FSL) v.s. 3dDWItoDT (AFNI)

3dDWItoDT: over 2000 lines c code - nonlinear fitting - take care the low SNR problem, FA values are in [0 1] range.

dtifit: only 551 lines c code (easy to understand) - linear fitting (straightforward) but the package itself will not take care of the low SNR problem in the dataset and generate FA values more than 1 which is physically impossible.

The following message is from dti-tk website: http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.Diffusivity

How to figure out the unit of diffusivity in a DTI volume?

If, for diffusion-weighting, b-value of 800 s.mm^-2 is used during the acquisition, and you input the number 800 as the b-value to your tensor reconstruction program, then the output DTI volume will have the unit of mm².s^-1.

Alternatively, you can compute the trace map of your DTI volumes. If you find that the trace values for CSF are close to 10^-2, then most likely it is in the unit of mm².s^-1.

For AFNI users: 3dDWtoDT in AFNI does NOT factor b-value into the tensor estimation (Read more here). As a result, the program essentially always assume the b-value to be equal to 1. If the actual b-value is 1,000 s.mm², then the equivalent unit of diffusivity used by 3dDWItoDT is the same as DTI-TK. If the actual b-value is 800 s.mm², then the equivalent unit of diffusivity is 1/800 mm².s^-1 instead. The multiplication factor should then be 1.25.
For Camino users: In general, it depends on how the scheme file is created. If the scheme file conforms to the default unit of Camino, the diffusivity unit should be m².s^-1.
For FSL users: If the correct b-value is used for the corresponding entries in the bval file, then the diffusivity unit should be mm².s^-1.