open-discussion > RE: DTIPrep on multi-shell data + DWMRI gradient mismatch error
Aug 14, 2020  06:08 PM | Steven Meisler - Harvard University / MIT
RE: DTIPrep on multi-shell data + DWMRI gradient mismatch error
Hi Maria,

1) What version of DTIPrep and DWIConvert are you using? Older versions tend to not preserve all the b-values. I use https://github.com/pnlbwh/conversion/tree/master/conversion to do my FSLtoNRRD conversions.

To my knowledge, the diffusion bcheck step is not too problematic. I usually disable it.

2) You may want to make sure your bval and bvec files are okay (DTIPrep may expect them in row or column format, and make sure they have the same number of elements). I have not come across that error yet.

3) Does that 59 index correspond to where your bval changes from 1000 to 2000 by any chance? Since image intensity changes with b-value, DTIPrep may be interpreting those high b-val scans as interlace-wise outliers. If so, you can change the protocol to make the interlace-wise check thresholds for gradients much more conservative, or disable the check altogether.

Does this makes sense?

Best,
Steven

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TitleAuthorDate
Maria Economou Aug 12, 2020
Maria Economou Sep 30, 2020
RE: DTIPrep on multi-shell data + DWMRI gradient mismatch error
Steven Meisler Aug 14, 2020
Martin Styner Aug 16, 2020