3D recon

KomaMRICore/src/rawdata/ISMRMRD.jl

@@ -85,19 +85,24 @@ function signal_to_raw_data(
     mink = minimum(ktraj, dims=1)
     maxk = maximum(ktraj, dims=1)
     Wk = maxk .- mink
-    Δx = 1 ./ Wk[1:2] #[m] Only x-y
+    Δx = 1 ./ Wk[1:3] #[m] Only x-y
     Nx = get(seq.DEF, "Nx", 1)
     Ny = get(seq.DEF, "Ny", 1)
     Nz = get(seq.DEF, "Nz", 1)
+    Nd_seq = (Nx > 1) + (Ny > 1) + (Nz > 1)
+    if ndims != Nd_seq; @warn("Seqfile is $Nd_seq dimensional but recon is $ndims."); end
     if haskey(seq.DEF, "FOV")
-        FOVx, FOVy, _ = seq.DEF["FOV"] #[m]
+        FOVx, FOVy, FOVz = seq.DEF["FOV"] #[m]
         if FOVx > 1 FOVx *= 1e-3 end #mm to m, older versions of Pulseq saved FOV in mm
         if FOVy > 1 FOVy *= 1e-3 end #mm to m, older versions of Pulseq saved FOV in mm
+        if FOVz > 1 FOVz *= 1e-3 end #mm to m, older versions of Pulseq saved FOV in mm
         Nx = round(Int64, FOVx / Δx[1])
         Ny = round(Int64, FOVy / Δx[2])
+        Nz = round(Int64, FOVy / Δx[3])
     else
         FOVx = Nx * Δx[1]
         FOVy = Ny * Δx[2]
+        FOVz = Nz * Δx[3]
     end
     #It needs to be transposed for the raw data
     ktraj = maximum(2*abs.(ktraj[:])) == 0 ? transpose(ktraj) : transpose(ktraj)./ maximum(2*abs.(ktraj[:]))
@@ -125,15 +130,15 @@ function signal_to_raw_data(
         # "trajectoryDescription"          => Dict{String, Any}("comment"=>""), #You can put wathever you want here: comment, bandwidth, MaxGradient_G_per_cm, MaxSlewRate_G_per_cm_per_s, interleaves, etc
         #encoding
         #   encodedSpace
-        "encodedSize"                    => [Nx, Ny, 1],                        #encodedSpace>matrixSize
-        "encodedFOV"                     => Float32.([FOVx, FOVy, 1e-3]*1e3),   #encodedSpace>fieldOfView_mm
+        "encodedSize"                    => [Nx, Ny, Nz],                        #encodedSpace>matrixSize
+        "encodedFOV"                     => Float32.([FOVx, FOVy, FOVz]*1e3),   #encodedSpace>fieldOfView_mm
         #   reconSpace
-        "reconSize"                      => [Nx+Nx%2, Ny+Ny%2, 1],              #reconSpace>matrixSize
-        "reconFOV"                       => Float32.([FOVx, FOVy, 1e-3]*1e3),   #reconSpace>fieldOfView_mm
+        "reconSize"                      => [Nx+Nx%2, Ny+Ny%2, Nz+Nz%2],              #reconSpace>matrixSize
+        "reconFOV"                       => Float32.([FOVx, FOVy, FOVz]*1e3),   #reconSpace>fieldOfView_mm
         #encodingLimits
         "enc_lim_kspace_encoding_step_0" => Limit(0, Nx-1, ceil(Int, Nx / 2)),  #min, max, center, e.g. phase encoding line number
         "enc_lim_kspace_encoding_step_1" => Limit(0, Ny-1, ceil(Int, Ny / 2)),  #min, max, center, e.g. partition encoding number
-        "enc_lim_kspace_encoding_step_2" => Limit(0, 0, 0),                     #min, max, center, e.g. partition encoding number
+        "enc_lim_kspace_encoding_step_2" => Limit(0, Nz-1, ceil(Int, Nz / 2)),  #min, max, center, e.g. partition encoding number
         "enc_lim_average"                => Limit(0, 0, 0),                     #min, max, center, e.g. signal average number
         "enc_lim_slice"                  => Limit(0, 0, 0),                     #min, max, center, e.g. imaging slice number
         "enc_lim_contrast"               => Limit(0, 0, 0),                     #min, max, center, e.g. echo number in multi-echo

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
-        Nx, Ny = raw_aux.params["reconSize"][1:2]
-        rec_params[:reconSize] = (Nx, Ny)
+        Nx, Ny, Nz = raw_aux.params["reconSize"][1:3]
+        rec_params[:reconSize] = (Nx, Ny, Nz)
         rec_params[:densityWeighting] = true
 
         # Perform reconstruction

src/ui/ExportUIFunctions.jl

@@ -120,7 +120,7 @@ end
 """
 Returns the default raw signal used by the UI.
 """
-function setup_raw()
+function setup_raw() # needs modifications for 3D?
 
     # Define the default RawAcquisitionData struct
     raw = RawAcquisitionData(