near-zero b-values

[tina.r...@gmail.com]

Hi,

I want to start some analysis on the HCP data. However, the bvalues in HCP are ~0, ~1000, ... instead of being exactly 0, 1000, etc. I think I should change the ~0 bvalues to zero in order to avoid the error: "All b=0 measurements are negative". I wanted to make sure that this is not a wrong thing to do. Moreover, should I change the ~1000 bvalues to 1000 and so on (in other words should they be treated the same way?) or it is better to have them as they are, for the matter of precision?

Any advice would be greatly appreciated.

Thank you very much in advance,

Regards,

Tina 

[Hui Zhang]

Hi Tina,

Indeed, with the current version, you will have to make sure that the b-values of the b=0's are all set to zero.  This should not have much or any effect on the results.

If you want to process the HCP data, a more important matter is to account for the spatially varying b-values and b-vectors.  The HCP data provides an extra volume in the Diffusion folder of each subject called grad_dev.nii.  This volume provides the adjustment that needs to be made to the b-value and b-vector for each voxel.

Gary

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[tina roostaei]

Hi Gary,

Thank you very much for the mindful tip. So, I assume that using these adapted codes the fitting will be performed using corrected b-values and b-vectors for each voxel: 

In FSL2Protocol_grad.m: line 1 is changed, lines 17 and 65 are commented.

In batch_fitting_single_grad.m: line 1 is changed, lines 23-36, and 86-101 are added.

I would be grateful if you could let me know whether there should be any further changes.

Thanks,

Tina

[tina roostaei]

Hi, 

Sorry, I should have commented out line 29 instead of line 28. Please find attached the new file.

Tina

[Hui Zhang]

Hi Tina,

Looks reasonable but I don't have time to actually test it out.  One thing to make sure is that the b=0's still have a b-value of 0 after your correction.

Gary