update doc

aTrotier · aTrotier · commit 779242587f38 · 2024-11-12T17:18:40.000+01:00
diff --git a/README.md b/README.md
@@ -9,14 +9,9 @@
 Rawdata for tests are available here : https://zenodo.org/records/14046657
 
 
-
-
 ---
 
 
-
-
-
 SEQ_BRUKER_a_MP2RAGE_CS_360.jl is a Julia package that implements a reconstruction for an accelerated MP2RAGE sequence for Bruker scanner (**PV360-3.5**). 
 The reconstruction is performed using MRIReco.jl 
 
@@ -32,7 +27,15 @@ Additionally, if you use the sequence available in the MR sequence folder, pleas
 
 ## Bruker sequence and protocol
 
-The sequence, implemented for **Bruker Paravision PV-360.3.5**, and the corresponding protocol for fully-sampled  is available in the folder  `MR sequence/PV-360.3.5`. Source code is available in this private directory : https://github.com/aTrotier/a_MP2RAGE_CS_360
+The sequence, implemented for **Bruker Paravision PV-360.3.5**, and the corresponding protocol for fully-sampled  is available in the folder  `MR sequence/PV-360.3.5`. 
+
+Compressed-sensing implementation is available through the standard Bruker tab `Resolution/Encoding`. If you want to perform a compressed-sensing experiment with an acceleration of 2 like the one used here : acceleration factor = 50% and use a calibration size of 5%
+```
+##$PVM_EncCSUndersampling=50
+##$PVM_EncCSCenterRatio=5
+```
+
+Source code is available in this private directory : https://github.com/aTrotier/a_MP2RAGE_CS_360
 
 ## Julia Installation
 
@@ -138,8 +141,6 @@ dir_path = "" # directory path where the files will be create
 write_bids_MP2RAGE(d,subject_name,dir_path)
 ```
 
-## Version
-
 
 [docs-img]: https://img.shields.io/badge/docs-latest%20release-blue.svg
 [docs-url]: https://crmsb.github.io/SEQ_BRUKER_a_MP2RAGE_CS_360/dev/
diff --git a/docs/make.jl b/docs/make.jl
@@ -20,6 +20,8 @@ makedocs(;
     ),
     pages=[
         "Home" => "index.md",
+        "Sequence and protocol" => "sequence.md",
+        "Installation and usage" => "reconstruction.md",
         "Examples" =>["generated/examples/simple_reco.md",
                         "generated/examples/advanced_reco.md"],
         "API" => "api.md"
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -1,3 +1,5 @@
+```@index
+```
 
 ```@autodocs
 Modules = [SEQ_BRUKER_a_MP2RAGE_CS_360]
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -4,7 +4,23 @@ CurrentModule = SEQ_BRUKER_a_MP2RAGE_CS_360
 
 # SEQ\_BRUKER\_A\_MP2RAGE\_CS\_360
 
-Documentation for [SEQ_BRUKER_a_MP2RAGE_CS_360](https://github.com/CRMSB/SEQ_BRUKER_a_MP2RAGE_CS_360.jl).
+SEQ_BRUKER_a_MP2RAGE_CS_360.jl is a Julia package that implements a reconstruction for an accelerated MP2RAGE sequence for Bruker scanner (**PV360-3.5**). 
+The reconstruction is performed using MRIReco.jl 
 
-```@index
-```
+More information and examples are available in the article [![][paper-img]][paper-url] and in the  [![][docs-img]][docs-url]
+
+## How to give credit
+
+If you use this package please acknowledge us by citing : https://doi.org/10.1002/mrm.27438
+
+Additionally, if you use the sequence available in the MR sequence folder, please contact us to sign the sequence transfer agreement : aurelien.trotier@rmsb.u-bordeaux.fr
+
+
+
+![](./docs/src/img/fig_explain.png)
+
+[docs-img]: https://img.shields.io/badge/docs-latest%20release-blue.svg
+[docs-url]: https://crmsb.github.io/SEQ_BRUKER_a_MP2RAGE_CS_360/dev/
+
+[paper-img]: https://img.shields.io/badge/doi-10.1002/mrm.27438-blue.svg
+[paper-url]: https://doi.org/10.1002/mrm.27438
diff --git a/docs/src/reconstruction.md b/docs/src/reconstruction.md
@@ -0,0 +1,31 @@
+
+# Package Installation
+
+You can install the package in any project with the following command :
+
+- launch julia with the command `julia`
+- enter the Julia package manager by typing `]` in the REPL. (the REPL should turn in blue)
+- if you want to activate an environment, type : `activate .` (otherwise the package will be installed in the global environment)
+- In order to add our unregistered package, type `add https://github.com/CRMSB/SEQ_BRUKER_a_MP2RAGE_CS_360`
+- if you want to use the package in your script just add the following line : `using SEQ_BRUKER_a_MP2RAGE_CS_360`
+
+
+# How to use the package
+
+Follow the example in the [documentation](https://crmsb.github.io/SEQ_BRUKER_a_MP2RAGE_CS_360/dev/generated/examples/simple_reco/) 
+
+**Steps :**
+- Define the path to the bruker dataset
+```julia
+path_bruker = joinpath(datadir, "MP2RAGE_FULLY")
+```
+- Perform the reconstruction 
+```julia
+d = reconstruction_MP2RAGE(path_bruker; mean_NR=true)
+```
+- write the results in the qBIDS format
+```julia
+subject_name = "sub_01"
+dir_path = "" # directory path where the files will be create
+write_bids_MP2RAGE(d,subject_name,dir_path)
+```
diff --git a/docs/src/sequence.md b/docs/src/sequence.md
@@ -0,0 +1,27 @@
+# Bruker sequence and protocol
+
+The sequence, implemented for **Bruker Paravision PV-360.3.5**, and the corresponding protocol for fully-sampled  is available in the folder  `MR sequence/PV-360.3.5`. 
+
+## Enable compressed-sensing acquisition
+
+Compressed-sensing implementation is available through the standard Bruker tab `Resolution/Encoding`. If you want to perform a compressed-sensing experiment with an acceleration of 2 like the one used here : acceleration factor = 50% and use a calibration size of 5%
+```
+##$PVM_EncCSUndersampling=50
+##$PVM_EncCSCenterRatio=5
+```
+
+## Source code
+
+Source code is available in this private directory : https://github.com/aTrotier/a_MP2RAGE_CS_360
+
+# Raw datasets
+
+The rawdata used in the example are stored on zenodo : https://zenodo.org/records/14046657
+- One is a fully sampled acquisition (128x128x96)
+- The other one is accelerated by a factor of 2
+```
+##$PVM_EncCSUndersampling=50
+##$PVM_EncCSCenterRatio=5
+```
+
+They are used for each merge to generate the figures used in examples.

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	+```@index
	`2`	+```
`1`	`3`
`2`	`4`	```@autodocs
`3`	`5`	`Modules = [SEQ_BRUKER_a_MP2RAGE_CS_360]`