Well, I think you would be better off, as far as ability to reconstruct multiple fibers and reducing your uncertainty of orientation estimations, to use a single shell at the maximum bvalue.  If you are using the data for other purposes than FSL probabilistic tractography that benefit from the lower shells, then that makes the picture more muddy. J 

 

To test to see how you are doing, you can compare your ability to reconstruct 2^nd fibers to that of the sample FSL dataset (at least I think FSL still distributes a 60 direction b=1000 sample dataset).  You can generate a quantitative measure of 2^nd fiber reconstructed by determining the number of 2^nd fibers with a volume fraction above a certain threshold (e.g. 0.05, i.e. mean_f2samples greater than 0.05) as a proportion of first fibers above that threshold.  For example, you could generate this ratio (#Voxels with mean_f2samples > 0.05) / (#Voxels with mean_f1samples > 0.05) and compare between the two datasets.  If you just want a rough estimate, you can do this on the files as they come out of bedpostx.  If you want to be a bit more accurate, you should make sure there aren’t any non-brain voxels or voxels in which not all directions have data (e.g. what happens on the slice at the edge of the FOV) after correction of subject motion and eddy currents (usually done by eroding the brain mask to remove these regions from the measurements you do with fslstats).  For reference: on the 256 direction dataset with b=1500 that was released for the Pittsburgh Competition I get 0.72 or 72% of white matter voxels have a second fiber above threshold.  If I recall correctly, this is similar to what one gets with a 60 direction b=1000 dataset, and the major differences are in number of 3^rd fibers and fiber uncertainty.  

 

Uncertainty is a bit more difficult to easily quantify with the released version of FSL, but I think the new version will have the option to output the dispersion of the fiber estimates in radians, though you may have to modify the bedpostx_postproc script to send that flag to make_dyadic_vectors.

 

In general, at least with the released version of FSL, one will do better as one uses more unique directions at a single higher bvalue in reconstructing subsidiary fibers and reducing uncertainty in fiber orientations.  As to whether non-single shell schemes can be exploited to do as well or better than single shell schemes is an unsolved question!

Peace,

 

Matt.

 

 

Average trace of bmatrix (sec/mm2)	Number of directions
3.8	3
8.5	6
64.9	10
114.3	12
348	16
574.6	18
858	20
1198	22

 

This is the scheme we used for thalamic segmentation, and I did not notice major abnormalities here with bedpostx, however I might have to look more carefully. What would be a good test of this?

In this case, would it be advisable to drop the intermediate shells (say b= 65-575?)? I thought that when we first consulted Tim about this, he advised to maintain the intermediate shells to gain SNR…. Stefano