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3D recon #324

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Commits on Mar 13, 2024

  1. 3D_recon work in progress. 

    modified:   ../KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   KomaUI.jl
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  2. Line 123 setup_raw() needs modifications for 3D? 

    modified:   ExportUIFunctions.jl
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Commits on Mar 24, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Mar 27, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Mar 30, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Apr 5, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Apr 8, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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  2. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on May 15, 2024

  1. Merge branch 'master' into 3D_recon

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Commits on Jun 4, 2024

  1. Merge branch 'master' into 3D_recon

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Commits on Jun 5, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jun 6, 2024

  1. Doctring updated for Sequence(). 

    modified:   KomaMRIBase/src/datatypes/Sequence.jl
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  2. Fixed typo in Sequence() docstring. 

    modified:   KomaMRIBase/src/datatypes/Sequence.jl
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  3. Now exporting default_sim_params. 

    modified:   KomaMRICore/src/KomaMRICore.jl
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Commits on Jun 7, 2024

  1. Changes to signal_to_raw_data, now separate counters for z and slices. 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  2. Fixed counter calculation for nz and ns for signal_to_raw_data. 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  3. Debugging counters for signal_to_raw_data. No need to reset the scan_… 

    …counter?

modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  4. Counters fixed. Needs some more testing. Ready to try 3D recon with M… 

    …RIReco. Need to configure reco_parameters.

modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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Commits on Jun 8, 2024

  1. Fixing 2D vs 3D in progress, 2D currently broken in KomaUI()!! 

    modified:   ISMRMRD.jl
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  2. Merge branch 'JuliaHealth:master' into 3D_recon

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  3. Still debugging... 

    modified:   ISMRMRD.jl
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  4. Merge branch '3D_recon' of github.com:curtcorum/KomaMRI.jl into 3D_recon

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  5. Still forces 2D recons someplace...???!!! 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   src/KomaUI.jl
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  6. Debugging reconstruction calls from KomaUI(). 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   src/KomaUI.jl
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  7. Debug raw data conversion for ge3d_cac.seq, something funny...!!! 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   src/KomaUI.jl
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Commits on Jun 10, 2024

  1. A fair amount of work to estimate proper 3D recon parameters from seq… 

    …, and work and debugging of the scan counters for 3D.

modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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Commits on Jun 12, 2024

  1. Update ISMRMRD.jl 

    Should fix test failure at:

https://github.com/JuliaHealth/KomaMRI.jl/blob/931fec8f318b247dfbc90fa33f0b598216f6a3c8/KomaMRICore/test/runtests.jl#L154-L158

Mentioned: JuliaHealth#324 (comment)

In draft PR: 3D recon
JuliaHealth#324
    @curtcorum
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  2. Merge branch 'JuliaHealth:master' into 3D_recon

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  3. Update ISMRMRD.jl 

    Added `use_ndseq` to `signal_to_raw_data()` docstring
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  4. Update ISMRMRD.jl 

    More updates for FOV estimation
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  5. Update ISMRMRD.jl 

    debugging
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  6. Update ISMRMRD.jl 

    One more debug?
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  7. Update ISMRMRD.jl

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  8. Debugging signal_to_raw_data 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  9. Check on Ny, Ns, Nz == 0 for scan counters. 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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Commits on Jun 13, 2024

  1. Defaulting to use_ndseq=true for signal_to_raw_data. 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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Commits on Jun 17, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jun 18, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jun 19, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jun 20, 2024

  1. Merge branch 'master' into 3D_recon

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Commits on Jun 24, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jul 8, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jul 9, 2024

  1. Working on central recon parameter estimation in KomaMRICore/src/rawd… 

    …ata/ISMRMRD.jl

modified:   KomaMRICore/src/KomaMRICore.jl
modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   KomaMRIFiles/src/Sequence/Pulseq.jl
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Commits on Jul 15, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jul 16, 2024

  1. Working on estimate_seq_recon_dimension, working for 2d multislice, n… 

    …ot for spiral

modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  2. Merge branch 'master' into 3D_recon 

    Conflicts: (fixed)
KomaMRICore/src/rawdata/ISMRMRD.jl

Changes to be committed:
modified:   KomaMRIBase/Project.toml
modified:   KomaMRIBase/src/KomaMRIBase.jl
modified:   KomaMRICore/Project.toml
modified:   KomaMRICore/src/KomaMRICore.jl
modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
modified:   KomaMRICore/src/simulation/SimulatorCore.jl
modified:   KomaMRICore/test/Project.toml
deleted:    KomaMRICore/test/initialize.jl
new file:   KomaMRICore/test/initialize_backend.jl
modified:   KomaMRICore/test/runtests.jl
modified:   KomaMRIFiles/Project.toml
modified:   KomaMRIFiles/src/KomaMRIFiles.jl
modified:   KomaMRIFiles/src/Phantom/Phantom.jl
modified:   KomaMRIPlots/Project.toml
modified:   KomaMRIPlots/src/KomaMRIPlots.jl
modified:   Project.toml
modified:   src/KomaMRI.jl
modified:   src/KomaUI.jl
    @curtcorum
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Commits on Jul 17, 2024

  1. Fixing merge. 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  2. Whitespace formatting. 

    modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  3. Forced type of Nx, Ny, Nz, Ns read from seq.DEF to be Int64. 

    Was not matching ::Tuple{Vararg{Int64, D}} in MRIBase ~/.julia/packages/MRIBase/GskMD/src/Datatypes/AcqData.jl:21
modified:   KomaMRICore/src/rawdata/ISMRMRD.jl
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  4. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Jul 18, 2024

  1. LiearAlgebra added to Project. Check for radial sampling. 

    Need to have Nx, etc. be sequence structure and send separate matrix size for recon parameters.
modified:   Project.toml
modified:   src/KomaMRICore.jl
modified:   src/rawdata/ISMRMRD.jl
modified:   ../Project.toml
    @curtcorum
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Commits on Aug 5, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Sep 1, 2024

  1. Merge branch 'master_merge' into 3D_recon_merge 

    Conflicts:
	KomaMRICore/src/simulation/GPUFunctions.jl
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Commits on Sep 27, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

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Commits on Oct 3, 2024

  1. Merge branch 'JuliaHealth:master' into 3D_recon

    @curtcorum
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