Pixel dimensions in TWIX data

[CWDAVIESJENKINS]

Hello Will,

I've been working on NFTI MRS voxel/structural co-registration using NIfTI MRS data generated by your amazing tool. I've been able to get this working for Philips data. However, I encountered an issue in the dimensions of the NIfTI generated from TWIX data. While the slice dimension is correctly parsed, it appears that the read/phase dimensions aren't. I had a look at the TWIX data using mapVBVD and it looks like the dimensions parsed might be:
[twix_obj.hdr.Config.RoFOV, twix_obj.hdr.Config.PhaseFoV, twix_obj.hdr.Config.VoI_SliceThickness]
rather than:
[twix_obj.hdr.Config.VoI_RoFOV, twix_obj.hdr.Config.VoI_PeFOV, twix_obj.hdr.Config.VoI_SliceThickness]

If I've overlooked something in spec2nii, then I'd really appreciate a shove in the right direction, but just wanted to raise this issue with you.

Thanks,
Chris

[wtclarke]

Hi Chris,

I believe the twix converter is the most well validated part of the tool. However I am completely open to having got something wrong, or that (as I've been finding out) not all twix files are formatted exactly the same. The latter being especially true with newer XA line scanners.

Have you got a specific example that you can share the data for?

[CWDAVIESJENKINS]

Hi Will

Thanks for the quick response!

I'm also completely open to a mistake on my end, but can't figure out where the issue is occurring... I've been using nii_tool from the dcm2nii repo (https://github.com/xiangruili/dicm2nii), but the issue seems to be occurring in FSLEYES, too. I can certainly share some data with you. I'll drop you an email once I've had a chance to organize it.

Thanks again,
Chris