From 779242587f38070c2eb047fc89f571f1cd44c58d Mon Sep 17 00:00:00 2001 From: aTrotier Date: Tue, 12 Nov 2024 17:18:40 +0100 Subject: [PATCH] update doc --- README.md | 17 +++++++++-------- docs/make.jl | 2 ++ docs/src/api.md | 2 ++ docs/src/index.md | 22 +++++++++++++++++++--- docs/src/reconstruction.md | 31 +++++++++++++++++++++++++++++++ docs/src/sequence.md | 27 +++++++++++++++++++++++++++ 6 files changed, 90 insertions(+), 11 deletions(-) create mode 100644 docs/src/reconstruction.md create mode 100644 docs/src/sequence.md diff --git a/README.md b/README.md index 0efdeaf..7d6cf34 100644 --- 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 index bbd6ccf..2205d7b 100644 --- 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 index 15e0bd3..a1a8184 100644 --- 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 index 264e1c0..2191cd5 100644 --- 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 \ No newline at end of file diff --git a/docs/src/reconstruction.md b/docs/src/reconstruction.md new file mode 100644 index 0000000..bb5b5e5 --- /dev/null +++ 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) +``` \ No newline at end of file diff --git a/docs/src/sequence.md b/docs/src/sequence.md new file mode 100644 index 0000000..1c14917 --- /dev/null +++ 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. \ No newline at end of file