Hopefully this manual for B0 unwarping with data from a philips scanner can be of use to you: https://osf.io/hks7x/
It took us quite some time to figure it out, but the results after correcting look good (we also ran it by Mark Jenkinson), so I'm happy that others can now use this and maybe even improve it. Please let me know if you have any questions or suggestions.
For the specific question of shifting voxels in the wrong direction; this may have to do with the scan you acquired, the last part of the manual briefly touches on that.
Anna van 't Veer
Hello,I re-discovered this old post about a S/I gradient in field maps from Philips scanners, as I'm currently looking at some Philips data which displays exactly the same issue. Did you ever manage to resolve it?Best wishes,IanOn 09/07/12 16:32, Michael Harms wrote:
My apologies for re-posting this one more time, but I'm really stumped.
I would REALLY appreciate it (and would be happy to treat you to a
beverage of your choice at the next OHBM) if someone that has
successfully acquired and applied field map correction from a Philips
Achieva could contact me with what they had to do.
I'd be happy to then summarize whatever I learn to the broader FSL-list.
On Fri, 2012-06-29 at 11:38 -0500, Michael Harms wrote:
Hello FEAT users with Philips scanners,
I would be highly appreciative if someone that has successfully applied
fieldmapping correction (B0 unwarping) using Philips scanner data would
contact me off the list so that I could pick your brain.
We have data from a multi-site study, of which one site was a Philips
scanner. I *thought* that I knew what needed to be done to apply
fieldmapping correction for the data from this site, but the comparison
in the Prestats report of "undistorted example_func to undistorted
fieldmap" clearly shows that we don't have something right.
The odd thing is that the "Unwarping shift map" from the Philips site
data shows a spatial pattern that is completely different from what we
observe from 4 different Siemens sites. Namely, it has a rather strong
S/I gradient, with negative voxel shifts inferiorly, and positive voxel
shifts superiorly. This makes me wonder if what we collected wasn't a
proper fieldmap (the site collected a FFE with "B0 field map = yes" and
"delta TE = 2.5 ms"), but if that's the case, I'd like to know what the
site needs to do differently at the time of acquisition.
Thanks in advance!