Hi all,

I have a large dataset (n>100) on which I want to apply DTIPrep for faster QC. Multi-shell diffusion data were acquired with the following scheme: b-values of 0,700,1000 and 2000 s/mm2 at 7,20,32 and 60 directions respectively. I used DWIConvert and the FSLtoNrrd flag to convert my data into the right format for DTIPrep. The protocol includes 2mm translation and 0.5 degrees rotation thresholds.

1) I was wondering if anyone has experience using DTIPrep on multi-shell data? I noticed that during at the diffusion bcheck step, the bvalue is set at 2000 - does this mean that DTIprep assumes all gradients were acquired with a single bvalue? And to what extend is this an issue?

2) I applied DTIPrep on a subset of subjects and after looking at some of the reports I noticed this error during the bvalue check step:
"DWMRI_gradient_0000 mismatch!". This error is present in most of the gradients (regardless of bvalue) in almost all subjects. To what extend is this problematic for further outlier detection steps?

What I also noticed was that in some subjects DTIPrep systematically only evaluated included gradients up to a certain number (59 in our dataset) without going through the entire dataset (119 gradients). Has anyone experienced this issue before or any other possible explanations?


Many thanks in advance for the feedback and don't hesitate to ask me for more information!

Best,
Maria