questions > RE: v20241211 - Philips diffusion enhanced scans
Jun 12, 2025  05:06 PM | Chris Rorden
RE: v20241211 - Philips diffusion enhanced scans

Your images look fine. The issue is that Siemens DWI scans ALWAYS start with a b=0 volume, while this is not the case for Philips. Therefore, old versions of dcm2niix would reorder Philips volumes to make the first volume the b=0, which allows you to neglect the final parameter for FSL’s eddy_correct:
   eddy_correct <4dinput> <4doutput> <reference_no>

However, modern versions of FSL’s eddy/topup assume that data is provided in the order temporarlly acquired, modelling motion for artifacts. Due to this, modern versions of dcm2niix do not reorder data. Regardless of which verion of dcm2niix you use, the bval and bvec orders correspond to the image order, so things should process fine, albeit the new FSL tools might give a slightly more precise answer for newer data.

Note that with the old dcm2niix, the first volume is bright (as b=0 has higher SNR), while the subsequent volumes are dark. With the new version, the reverse is true, which you can see with the intensity timeline below.

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TitleAuthorDate
csee Jun 11, 2025
RE: v20241211 - Philips diffusion enhanced scans
Chris Rorden Jun 12, 2025
Chris Rorden Jun 11, 2025