add offsets for bruker sequence

[aTrotier]

Offset correction for Bruker data.

Works on :

• Axial + L_R
• Coronal + H_F
• Sagital + H_F

TO DO :

• [x] test with other direction
• [x] Oblique acquisition
• [ ] 2D ?
• [ ] add tests

Remarks / question :

1) maybe a slight offset by one voxel due to the way bruker performs the FFT ? 2) Bruker only need to correct the offset along Phase1/phase2 (not read), how do you want to manages that ? For now the offset correction is performed under AcquisitionData(). Do you prefer to create a dedicated function object that takes either the AcquisitionData or RawData, correct the offset along R/P/S according to a tuple (False,True,True) ? 3) a permutation along the data is required between the 2dseq and the reconstructed image.

# Permute according to direction
if b["PVM_FovSatSliceOri"][1] == "axial"
    @info "axial"
    Isos_cor = permutedims(Isos_cor,(2,1,3,4,5))

elseif b["PVM_FovSatSliceOri"][1] == "coronal"
    @info "coronal"

elseif b["PVM_FovSatSliceOri"][1] == "sagittal"
    @info "sagittal"
    Isos_cor = permutedims(Isos_cor, (2,1,3,4,5))
end

[codecov-commenter]

Codecov Report

Merging #90 (2025f5d) into master (7437e5b) will not change coverage. The diff coverage is n/a.

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  Hits          999      999           
  Misses        555      555           

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[aTrotier]

I think it is ready. Do you have some remarks

I have some questions :

1. I have multiple datasets with oblique plan along axial/coro/sag each with 2 read orientations AP/HF/LR. Maybe we can only use one of them for the test ?
2. Where should I put correctOffset(acq::AcquisitionData,offsetCor=[0,0,0])
3. I think the read/phase/slice direction and head position and fov should be in mm according to : https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h#L286. Do you want to change that ? (maybe it is better to do that in another PR)

I might give it a try directly on my scanner

[aTrotier]

I try it directly on the scanner and it seems to work even in other position that head_supine .