forget api and remove channel dimension

Author: aTrotier

docs/lit/examples/advanced_reco.jl

@@ -47,17 +47,17 @@ d_under = reconstruction_MP2RAGE(path_bruker; mean_NR=true)
 begin
   f = Figure(size=(500,400))
   ax=Axis(f[1,1],title="TI₁ undersampled")
-  h=heatmap!(ax,abs.(d_under["im_reco"][:,:,60,1,1,1]),colormap=:grays)
+  h=heatmap!(ax,abs.(d_under["im_reco"][:,:,60,1,1]),colormap=:grays)
 
   ax=Axis(f[1,2],title="TI₁ CS")
-  h=heatmap!(ax,abs.(d["im_reco"][:,:,60,1,1,1]),colormap=:grays)
+  h=heatmap!(ax,abs.(d["im_reco"][:,:,60,1,1]),colormap=:grays)
 
 
   ax=Axis(f[2,1],title="T₁ map undersampled")
-  h=heatmap!(ax,d_under["T1map"][:,:,60,1,1],colorrange = (500,2000))
+  h=heatmap!(ax,d_under["T1map"][:,:,60,1],colorrange = (500,2000))
 
   ax=Axis(f[2,2],title="T₁ map CS")
-  h=heatmap!(ax,d["T1map"][:,:,60,1,1],colorrange = (500,2000))
+  h=heatmap!(ax,d["T1map"][:,:,60,1],colorrange = (500,2000))
 
   for ax in f.content   # hide decoration befor adding colorbar
     hidedecorations!(ax)

docs/lit/examples/simple_reco.jl

@@ -29,32 +29,32 @@ d = reconstruction_MP2RAGE(path_bruker; mean_NR=true)
 
 
 # the result is a dictionnary with the following fields :
-# - "im_reco" : (x,y,z,Number of Channel , Number of Repetition,TI) Complex
-# - "MP2RAGE" : (x,y,z,Number of Channel , Number of Repetition) Float
-# - "T1map" : (x,y,z,Number of Channel , Number of Repetition) Float
+# - "im_reco" : (x,y,z, Number of Repetition,TI) Complex
+# - "MP2RAGE" : (x,y,z , Number of Repetition) Float
+# - "T1map" : (x,y,z , Number of Repetition) Float
 # - "params_prot"
 # - "params_reco"
 # - "params_MP2RAGE"
 # 
-# im_reco corresponds to the TI₁ and TI₂ images in the complex format with 6 dimensions :
-# (x,y,z, Number of Channel , Number of Repetition,TI)
+# im_reco corresponds to the TI₁ and TI₂ images in the complex format with 5 dimensions :
+# (x,y,z , Number of Repetition,TI). Channels are combined during the reconstruction
 
 
 # We can check the results
 
 begin
   f = Figure(size=(500,400))
   ax=Axis(f[1,1],title="TI₁")
-  h=heatmap!(ax,abs.(d["im_reco"][:,:,60,1,1,1]),colormap=:grays)
+  h=heatmap!(ax,abs.(d["im_reco"][:,:,60,1,1]),colormap=:grays)
 
   ax=Axis(f[1,2],title="TI₂")
-  h=heatmap!(ax,abs.(d["im_reco"][:,:,60,1,1,2]),colormap=:grays)
+  h=heatmap!(ax,abs.(d["im_reco"][:,:,60,1,2]),colormap=:grays)
 
   ax=Axis(f[2,1],title="UNIT1 / MP2RAGE")
-  h=heatmap!(ax,d["MP2RAGE"][:,:,60,1,1],colormap=:grays)
+  h=heatmap!(ax,d["MP2RAGE"][:,:,60,1],colormap=:grays)
 
   ax=Axis(f[2,2],title="T₁ map")
-  h=heatmap!(ax,d["T1map"][:,:,60,1,1],colorrange = (500,2000))
+  h=heatmap!(ax,d["T1map"][:,:,60,1],colorrange = (500,2000))
 
   for ax in f.content   # hide decoration befor adding colorbar
     hidedecorations!(ax)

docs/src/api.md

@@ -0,0 +1,4 @@
+
+```@autodocs
+Modules = [SEQ_BRUKER_a_MP2RAGE_CS_360]
+```

docs/src/index.md

@@ -2,13 +2,9 @@
 CurrentModule = SEQ_BRUKER_a_MP2RAGE_CS_360
 ```
 
-# SEQ\_BRUKER\_a\_MP2RAGE\_CS\_360
+# SEQ\_BRUKER\_A\_MP2RAGE\_CS\_360
 
-Documentation for [SEQ_BRUKER_a_MP2RAGE_CS_360](https://github.com/aTrotier/SEQ_BRUKER_a_MP2RAGE_CS_360.jl).
+Documentation for [SEQ_BRUKER_a_MP2RAGE_CS_360](https://github.com/CRMSB/SEQ_BRUKER_a_MP2RAGE_CS_360.jl).
 
 ```@index
 ```
-
-```@autodocs
-Modules = [SEQ_BRUKER_a_MP2RAGE_CS_360]
-```

src/BIDS.jl

@@ -8,9 +8,9 @@ This function writes data from a dictionary (`d`) in BIDS (Brain Imaging Data St
 **Arguments:**
 
 * `d` (Dict): A dictionary containing the data to be written. Expected key-value pairs:
-    * `im_reco` (Array): 5D array containing the reconstructed images.
-    * `MP2RAGE` (Array): Combined MP2RAGE image data.
-    * `T1map` (Array): Calculated T1 map from MP2RAGE images.
+    * `im_reco` (Array): 5D array containing the reconstructed images (x,y,z,NR,TI)
+    * `MP2RAGE` (Array): Combined MP2RAGE image data. (x,y,z,NR)
+    * `T1map` (Array): Calculated T1 map from MP2RAGE images. (x,y,z,NR)
     * `params_prot` (Dict): Protocol parameters extracted from the Bruker file.
     * `params_MP2RAGE` (Struct): Dictionary containing MP2RAGE specific parameters.
 
@@ -52,12 +52,12 @@ function write_bids_MP2RAGE(d::Dict,subname::AbstractString,folder="")
               "_UNIT1",
               "_T1map"]
 
-  data_ = [ abs.(d["im_reco"][:,:,:,1,:,1]),
-            angle.(d["im_reco"][:,:,:,1,:,1]),
-            d["im_reco"][:,:,:,1,:,1],
-            abs.(d["im_reco"][:,:,:,1,:,2]),
-            angle.(d["im_reco"][:,:,:,1,:,2]),
-            d["im_reco"][:,:,:,1,:,2],
+  data_ = [ abs.(d["im_reco"][:,:,:,:,1]),
+            angle.(d["im_reco"][:,:,:,:,1]),
+            d["im_reco"][:,:,:,:,1],
+            abs.(d["im_reco"][:,:,:,:,2]),
+            angle.(d["im_reco"][:,:,:,:,2]),
+            d["im_reco"][:,:,:,:,2],
             d["MP2RAGE"],
             d["T1map"]]
 

src/reconstruction.jl

@@ -12,7 +12,7 @@ Reconstructs MP2RAGE MRI data from a specified Bruker file path, returning image
 
 # Returns
 A dictionary with the following key-value pairs:
-- `"im_reco"`: Reconstructed MP2RAGE image array, permuted to match the expected order.
+- `"im_reco"`: Reconstructed MP2RAGE image array, permuted to match the expected order (x,y,z,number of Channel, Number of repetition)
 - `"MP2RAGE"`: Combined MP2RAGE image data.
 - `"T1map"`: Calculated T1 map from MP2RAGE images.
 - `"params_reco"`: Dictionary of parameters used for reconstruction.
@@ -59,12 +59,13 @@ function reconstruction_MP2RAGE(path_bruker;mean_NR::Bool = false,paramsCS=Dict(
 
   x_approx = reconstruction(acq, params).data
   if mean_NR
-    x_approx = mean(x_approx,dims=6)
+    x_approx = mean(x_approx,dims=6) # average accross repetition
   end
-  x_approx = permutedims(x_approx,(1,2,3,5,6,4))
+  x_approx = permutedims(x_approx,(1,2,3,5,6,4)) # permute to put contrast in last dimension
+  x_approx = x_approx[:,:,:,1,:,:] # remove coil dimension
 
   ## process data to extract T1 maps
-  MP2 = mp2rage_comb(x_approx[:,:,:,:,:,:])
+  MP2 = mp2rage_comb(x_approx)
 
   p = params_from_seq(b)