3D recon #324

curtcorum · 2024-03-13T03:26:04Z

Draft pull request for enabling 3D reconstruction.

See discussion: Reconstruction for 3D sequences #323

modified: ../KomaMRICore/src/rawdata/ISMRMRD.jl modified: KomaUI.jl

modified: ExportUIFunctions.jl

curtcorum · 2024-03-13T03:36:09Z

Managed to break 2D...looks like separate handling of 2D vs 3D is required in each function.

Probably best to do non_ui funnctions first, test, then ui functions.

shell> git branch -v
* 3D_recon          674c0f2 Line 123 setup_raw() needs modifications for 3D? modified:   ExportUIFunctions.jl
  ccdev             f0bfc86 Working on HSn....lots of problems. modified:   KomaMRIBase/src/sequences/PulseDesigner.jl
  master            0a8a93d Update README.md
  phantom_info      a86b7bb Merge branch 'JuliaHealth:master' into upsample_phantoms
  upsample_phantoms a86b7bb Merge branch 'JuliaHealth:master' into upsample_phantoms

Progress: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:44
  simulated_blocks:  22
  rf_blocks:         1
  acq_samples:       10201
 44.835454 seconds (43.57 M allocations: 2.874 GiB, 2.96% gc time, 86.70% compilation time: <1% of which was recompilation)
[ Info: Exporting to ISMRMRD file: /tmp/Koma_signal.mrd
[ Info: Running reconstruction ...
ArgumentError: Nodes x have dimension 2 != 3
Stacktrace:
  [1] initParams(k::Matrix{Float64}, N::Tuple{Int64, Int64, Int64}, dims::UnitRange{Int64}; kargs::Base.Pairs{Symbol, Int64, Tuple{Symbol, Symbol}, NamedTuple{(:m, :σ), Tuple{Int64, Int64}}})
    @ NFFT ~/.julia/packages/NFFT/RT2hs/src/precomputation.jl:20
  [2] initParams
    @ ~/.julia/packages/NFFT/RT2hs/src/precomputation.jl:3 [inlined]
  [3] NFFT.NFFTPlan(k::Matrix{Float64}, N::Tuple{Int64, Int64, Int64}; dims::UnitRange{Int64}, fftflags::Nothing, kwargs::Base.Pairs{Symbol, Int64, Tuple{Symbol, Symbol}, NamedTuple{(:m, :σ), Tuple{Int64, Int64}}})
    @ NFFT ~/.julia/packages/NFFT/RT2hs/src/implementation.jl:78
  [4] NFFTPlan
    @ ~/.julia/packages/NFFT/RT2hs/src/implementation.jl:73 [inlined]
  [5] macro expansion
    @ ~/.julia/packages/NFFT/RT2hs/src/NFFT.jl:49 [inlined]
  [6] macro expansion
    @ ./timing.jl:393 [inlined]
  [7] #plan_nfft#130
    @ ~/.julia/packages/NFFT/RT2hs/src/NFFT.jl:48 [inlined]
  [8] plan_nfft
    @ ~/.julia/packages/NFFT/RT2hs/src/NFFT.jl:46 [inlined]
  [9] #plan_nfft#2
    @ ~/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:13 [inlined]
 [10] plan_nfft
    @ ~/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:13 [inlined]
 [11] samplingDensity(acqData::AcquisitionData{Float32, 2}, shape::Tuple{Int64, Int64, Int64})
    @ MRIBase ~/.julia/packages/MRIBase/oNfYy/src/Datatypes/AcqData.jl:288
 [12] setupDirectReco(acqData::AcquisitionData{Float32, 2}, recoParams::Dict{Symbol, Any})
    @ MRIReco ~/src/MRIReco.jl/src/Reconstruction/RecoParameters.jl:19
 [13] reconstruction(acqData::AcquisitionData{Float32, 2}, recoParams::Dict{Symbol, Any})
    @ MRIReco ~/src/MRIReco.jl/src/Reconstruction/Reconstruction.jl:37
 [14] macro expansion
    @ ./timing.jl:501 [inlined]
 [15] (::KomaMRI.var"#61#97"{Dict{Symbol, Any}, Blink.AtomShell.Window})(#unused#::Int64)
    @ KomaMRI ~/src/KomaMRI/src/KomaUI.jl:230
 [16] #invokelatest#2
    @ ./essentials.jl:819 [inlined]
 [17] invokelatest
    @ ./essentials.jl:816 [inlined]
 [18] handle_message(o::Blink.Page, m::Dict{String, Any})
    @ Blink ~/.julia/packages/Blink/tnO3a/src/rpc/callbacks.jl:7
 [19] macro expansion
    @ ~/.julia/packages/Lazy/9Xnd3/src/macros.jl:268 [inlined]
 [20] ws_handler(ws::HTTP.WebSockets.WebSocket)
    @ Blink ~/.julia/packages/Blink/tnO3a/src/content/server.jl:50
 [21] (::Mux.var"#9#10"{Mux.App})(sock::HTTP.WebSockets.WebSocket)
    @ Mux ~/.julia/packages/Mux/PipQ9/src/server.jl:48
 [22] upgrade(f::Mux.var"#9#10"{Mux.App}, http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.Connections.Connection{Sockets.TCPSocket}}; suppress_close_error::Bool, maxframesize::Int64, maxfragmentation::Int64, kw::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ HTTP.WebSockets ~/.julia/packages/HTTP/1EWL3/src/WebSockets.jl:440
 [23] upgrade
    @ ~/.julia/packages/HTTP/1EWL3/src/WebSockets.jl:420 [inlined]
 [24] (::Mux.var"#14#15"{Mux.App, Mux.App})(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.Connections.Connection{Sockets.TCPSocket}})
    @ Mux ~/.julia/packages/Mux/PipQ9/src/server.jl:81
 [25] #invokelatest#2
    @ ./essentials.jl:819 [inlined]
 [26] invokelatest
    @ ./essentials.jl:816 [inlined]
 [27] handle_connection(f::Function, c::HTTP.Connections.Connection{Sockets.TCPSocket}, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
    @ HTTP.Servers ~/.julia/packages/HTTP/1EWL3/src/Servers.jl:456
 [28] macro expansion
    @ ~/.julia/packages/HTTP/1EWL3/src/Servers.jl:388 [inlined]
 [29] (::HTTP.Servers.var"#16#17"{Mux.var"#14#15"{Mux.App, Mux.App}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.Connections.Connection}, Int64, Nothing, Base.Semaphore, HTTP.Connections.Connection{Sockets.TCPSocket}})()
    @ HTTP.Servers ./task.jl:514

cncastillo · 2024-03-13T11:43:59Z

Thanks @curtcorum for all the effort!! This is similar to what I would have tried. I will try to take a further look asap.

cncastillo · 2024-03-13T11:46:00Z

src/KomaUI.jl

@@ -221,8 +221,8 @@ function KomaUI(; darkmode=true, frame=true, phantom_mode="2D", sim=Dict{String,
        acq_data = AcquisitionData(raw_aux)
        acq_data.traj[1].circular = false #Removing circular window
        acq_data.traj[1].nodes = acq_data.traj[1].nodes[1:2,:] ./ maximum(2*abs.(acq_data.traj[1].nodes[:])) #Normalize k-space to -.5 to .5 for NUFFT


Maybe this line is generating problems.

Suggested change

acq_data.traj[1].nodes = acq_data.traj[1].nodes[1:2,:] ./ maximum(2*abs.(acq_data.traj[1].nodes[:])) #Normalize k-space to -.5 to .5 for NUFFT

acq_data.traj[1].nodes = acq_data.traj[1].nodes[1:3,:] ./ maximum(2*abs.(acq_data.traj[1].nodes[:])) #Normalize k-space to -.5 to .5 for NUFFT

cncastillo · 2024-03-13T11:57:55Z

KomaMRICore/src/rawdata/ISMRMRD.jl

        Nx = round(Int64, FOVx / Δx[1])
        Ny = round(Int64, FOVy / Δx[2])
+        Nz = round(Int64, FOVy / Δx[3])


The Ci gives an error saying that NadcsPerImage = floor(Int, Nadcs / Nz) => Nz = 0. This line could be the problem.

Suggested change

Nz = round(Int64, FOVy / Δx[3])

Nz = round(Int64, FOVz / Δx[3])

I wonder if Δx[3] is Inf.

curtcorum · 2024-03-13T20:21:02Z

@cncastillo

Thanks @curtcorum for all the effort!! This is similar to what I would have tried. I will try to take a further look asap.

Thanks and my pleasure, Carlos!

I'm very interested in doing 3D simulation, especially of 3D Radial sequences, anything I can do to help.

I certainly greatly appreciate your, @beorostica, and the other developers and users work on KomaMRI!

curtcorum · 2024-03-20T01:11:23Z

Some comments/notes on 3D.

The UI and plots get bogged down with large seq and raw files.

It is potentially desirable for the UI to parameterize the maximum range of sequence blocks (or time range) for the seq slider. Then one could have a second slider, or stop rendering the slider and just show the range displayed in the main seq window. Not sure how to do this but something to think about.

Also there are similar UI or plot slowing down issues when the 2D or 3D phantom has a lot of points.

For the UI it might make sense to have some default and changeable parameters passed to KomaUI() in the manner of sim= and rec=:

ui_params = Dict{String,Any}()

'max_blocks', 500 # these are guesses for now

'max_raw', 2000

'max_points', 25000 # could sub-sample after some threshold

...

cncastillo · 2024-03-20T13:51:04Z

The UI and plots get bogged down with large seq and raw files.

You are absolutly right. I would just add ⬅️ ➡️ buttons and always render a max of 100 blocks maybe? The same could be done for plot_raw. @pvillacorta has played with something similar in #184 (f19a750).

I was imagining something like this

https://community.home-assistant.io/t/plotly-interactive-graph-card/347746

Not sure if this solution will fix the problem.

modified: KomaMRIBase/src/datatypes/Sequence.jl

modified: KomaMRICore/src/KomaMRICore.jl

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

…counter? modified: KomaMRICore/src/rawdata/ISMRMRD.jl

…RIReco. Need to configure reco_parameters. modified: KomaMRICore/src/rawdata/ISMRMRD.jl

modified: ISMRMRD.jl

More updates for FOV estimation

debugging

One more debug?

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

curtcorum · 2024-06-12T23:49:43Z

Local tests* of KomaMRICore went ok on Ubuntu 20.04

Linux green 5.15.0-107-generic #117~20.04.1-Ubuntu SMP Tue Apr 30 10:35:57 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Precompiling project...
  ✗ Metal → BFloat16sExt
  201 dependencies successfully precompiled in 97 seconds. 9 already precompiled.
  2 dependencies had output during precompilation:
┌ AbstractNFFTs
│  WARNING: method definition for #plan_nfft#3 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:16 declares type variable D but does not use it.
│  WARNING: method definition for #plan_nfft#4 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:21 declares type variable D but does not use it.
│  WARNING: method definition for #plan_nfct#8 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:16 declares type variable D but does not use it.
│  WARNING: method definition for #plan_nfct#9 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:21 declares type variable D but does not use it.
│  WARNING: method definition for #plan_nfst#13 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:16 declares type variable D but does not use it.
│  WARNING: method definition for #plan_nfst#14 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:21 declares type variable D but does not use it.
│  WARNING: method definition for #plan_nnfft#17 at /home/curt/.julia/packages/AbstractNFFTs/Xd3qS/src/derived.jl:34 declares type variable D but does not use it.
└  
┌ AMDGPU
│  WARNING: Wrapping `Vararg` directly in UnionAll is deprecated (wrap the tuple instead).
│  You may need to write `f(x::Vararg{T})` rather than `f(x::Vararg{<:T})` or `f(x::Vararg{T}) where T` instead of `f(x::Vararg{T} where T)`.
│  WARNING: Wrapping `Vararg` directly in UnionAll is deprecated (wrap the tuple instead).
│  You may need to write `f(x::Vararg{T})` rather than `f(x::Vararg{<:T})` or `f(x::Vararg{T}) where T` instead of `f(x::Vararg{T} where T)`.
└  
     Testing Running tests...
┌ Warning: Estimating FOV parameters from seq.DEF Nx, Ny, Nz and traj.
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:301
┌ Debug: Nd_seq = 2
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:308
┌ Debug: Nx, Ny, Nz, Ns = 101, 101, 1, 1
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:309
┌ Debug: FOVx, FOVy, FOVz = 0.23229999999419157, 0.2323000000111597, 1
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:310
┌ Debug: Δx, size( ktraj) = [0.002299999999942491, 0.002300000000110492, 1.0e-6], (10201, 3)
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:311
[ Info: Creating 2D ISMRMRD file ...
┌ Debug: Nd_seq = 2
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:308
┌ Debug: Nx, Ny, Nz, Ns = 101, 101, 0, 1
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:309
┌ Debug: FOVx, FOVy, FOVz = 0.23, 0.23, 0.0
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:310
┌ Debug: Δx, size( ktraj) = [0.002299999999942491, 0.002300000000110492, 1.0e-6], (10201, 3)
└ @ KomaMRICore ~/src/KomaMRI/KomaMRICore/src/rawdata/ISMRMRD.jl:311
[ Info: Creating 2D ISMRMRD file ...
Test Summary: | Pass  Total     Time
Package       |   81     81  2m17.6s

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

curtcorum · 2024-06-19T23:00:59Z

Probably the checks on the recon parameters should be moved to one place?

#409 (comment)

cncastillo · 2024-06-19T23:17:01Z

Yeah it should be its own function. Currently we are finishing of #411 and #408, and I can go back to the sequences and this.

…ata/ISMRMRD.jl modified: KomaMRICore/src/KomaMRICore.jl modified: KomaMRICore/src/rawdata/ISMRMRD.jl modified: KomaMRIFiles/src/Sequence/Pulseq.jl

…ot for spiral modified: KomaMRICore/src/rawdata/ISMRMRD.jl

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

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Was not matching ::Tuple{Vararg{Int64, D}} in MRIBase ~/.julia/packages/MRIBase/GskMD/src/Datatypes/AcqData.jl:21 modified: KomaMRICore/src/rawdata/ISMRMRD.jl

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

Conflicts: KomaMRICore/src/simulation/GPUFunctions.jl

curtcorum added 2 commits March 12, 2024 22:21

3D_recon work in progress.

36408a2

modified: ../KomaMRICore/src/rawdata/ISMRMRD.jl modified: KomaUI.jl

Line 123 setup_raw() needs modifications for 3D?

674c0f2

modified: ExportUIFunctions.jl

curtcorum requested a review from cncastillo as a code owner March 13, 2024 03:26

curtcorum marked this pull request as draft March 13, 2024 03:26

cncastillo reviewed Mar 13, 2024

View reviewed changes

curtcorum and others added 7 commits March 24, 2024 16:06

Merge branch 'JuliaHealth:master' into 3D_recon

d3ff944

Merge branch 'JuliaHealth:master' into 3D_recon

826fa5e

Merge branch 'JuliaHealth:master' into 3D_recon

6368e89

Merge branch 'JuliaHealth:master' into 3D_recon

be10215

Merge branch 'JuliaHealth:master' into 3D_recon

b1ce21c

Merge branch 'JuliaHealth:master' into 3D_recon

a7fd74e

Merge branch 'master' into 3D_recon

c6c9e21

cncastillo linked an issue May 17, 2024 that may be closed by this pull request

Reconstruction for 3D sequences #323

Open

curtcorum added 11 commits June 3, 2024 21:19

Merge branch 'master' into 3D_recon

8eb57a9

Merge branch 'JuliaHealth:master' into 3D_recon

f7a7c0b

Doctring updated for Sequence().

440402d

modified: KomaMRIBase/src/datatypes/Sequence.jl

Fixed typo in Sequence() docstring.

971bca4

modified: KomaMRIBase/src/datatypes/Sequence.jl

Now exporting default_sim_params.

43f01dd

modified: KomaMRICore/src/KomaMRICore.jl

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

c669ecc

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Fixed counter calculation for nz and ns for signal_to_raw_data.

032c3f2

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Debugging counters for signal_to_raw_data. No need to reset the scan_…

38fd47a

…counter? modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Counters fixed. Needs some more testing. Ready to try 3D recon with M…

aa37f37

…RIReco. Need to configure reco_parameters. modified: KomaMRICore/src/rawdata/ISMRMRD.jl

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

410c403

modified: ISMRMRD.jl

Merge branch 'JuliaHealth:master' into 3D_recon

b5fc898

curtcorum added 6 commits June 12, 2024 16:57

Update ISMRMRD.jl

9aac620

More updates for FOV estimation

Update ISMRMRD.jl

05d862a

debugging

Update ISMRMRD.jl

8719f0a

One more debug?

Update ISMRMRD.jl

acc981d

Debugging signal_to_raw_data

eb9b789

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Check on Ny, Ns, Nz == 0 for scan counters.

9f25e24

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Defaulting to use_ndseq=true for signal_to_raw_data.

26c6c1b

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

cncastillo mentioned this pull request Jun 14, 2024

An error of 'DivideError: integer division' occurs in the internal functions of simulate when using a sequence with spiral acquisition #409

Open

curtcorum added 3 commits June 17, 2024 15:29

Merge branch 'JuliaHealth:master' into 3D_recon

32b5dfd

Merge branch 'JuliaHealth:master' into 3D_recon

8b46d5c

Merge branch 'JuliaHealth:master' into 3D_recon

df5aff8

curtcorum added 16 commits June 20, 2024 18:21

Merge branch 'master' into 3D_recon

aba7452

Merge branch 'JuliaHealth:master' into 3D_recon

8f3fc9f

Merge branch 'JuliaHealth:master' into 3D_recon

6eb7702

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

585304f

…ata/ISMRMRD.jl modified: KomaMRICore/src/KomaMRICore.jl modified: KomaMRICore/src/rawdata/ISMRMRD.jl modified: KomaMRIFiles/src/Sequence/Pulseq.jl

Merge branch 'JuliaHealth:master' into 3D_recon

ffea298

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

af870bd

…ot for spiral modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Fixing merge.

12e0d63

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Whitespace formatting.

b101fe1

modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Forced type of Nx, Ny, Nz, Ns read from seq.DEF to be Int64.

c98d92b

Was not matching ::Tuple{Vararg{Int64, D}} in MRIBase ~/.julia/packages/MRIBase/GskMD/src/Datatypes/AcqData.jl:21 modified: KomaMRICore/src/rawdata/ISMRMRD.jl

Merge branch 'JuliaHealth:master' into 3D_recon

18539d1

LiearAlgebra added to Project. Check for radial sampling.

0f317cb

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

Merge branch 'JuliaHealth:master' into 3D_recon

3d5c2cc

Merge branch 'master_merge' into 3D_recon_merge

af4f6da

Conflicts: KomaMRICore/src/simulation/GPUFunctions.jl

Merge branch 'JuliaHealth:master' into 3D_recon

5bcff4f

Merge branch 'JuliaHealth:master' into 3D_recon

f393f4a

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3D recon #324

3D recon #324

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	acq_data.traj[1].nodes = acq_data.traj[1].nodes[1:2,:] ./ maximum(2*abs.(acq_data.traj[1].nodes[:])) #Normalize k-space to -.5 to .5 for NUFFT
	acq_data.traj[1].nodes = acq_data.traj[1].nodes[1:3,:] ./ maximum(2*abs.(acq_data.traj[1].nodes[:])) #Normalize k-space to -.5 to .5 for NUFFT

	Nz = round(Int64, FOVy / Δx[3])
	Nz = round(Int64, FOVz / Δx[3])

3D recon #324

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3D recon #324

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