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.
Threaded View
Title | Author | Date |
---|---|---|
csee | Jun 11, 2025 | |
Chris Rorden | Jun 12, 2025 | |
Chris Rorden | Jun 11, 2025 | |