SOSP_VASO

Stack of Spirals SS-SI-VASO

Prerequisits:

Install Docker Engine (https://docs.docker.com/engine/install/ubuntu/)

To perform the SOSP reconstruction:

1. Clone this repository: bash git clone https://github.com/monreal93/SOSP_VASO.git your_path/sosp_vaso/
2. Download the example data from: https://drive.google.com/drive/folders/1L4Dyr4P-co6K44CBIfmMfJGe2vqBTgOR?usp=sharing and save data folder into your_path/sosp_vaso/
3. Pull docker Julia docker with MRIReco.jl installed using the following command: docker pull monreal93/julia_mri_recon:latest
4. Start the cointainer with the following command:

   sudo docker run -t -d -P -v your_path/sosp_vaso:/usr/share/sosp_vaso --name julia_mri_recon monreal93/julia_mri_recon 
   # replace "/mnt/5T3/Alejandro/sosp_vaso" with local folder where data downloaded from Dropbox is located
   

5. Create julia startup file:

   sudo docker exec -it julia_mri_recon bash
   apt-get update
   apt-get install nano
   cd ~
   mkdir .julia/config/
   nano .julia/config/startup.jl
   # In nano editor
   cd("/usr/share/sosp_vaso/recon")  
   using Pkg
   if isfile("Project.toml") && isfile("Manifest.toml") 
    Pkg.activate(".") 
   end
   #
   exit

6. Enter julia and instal required packages:

sudo docker exec -it julia_mri_recon julia -t auto
Pkg.instantiate()

Perform the reconstruction

1. you can open and modify the file /sosp_vaso/recon/reconstructions.jl and modify the reconstruction parameters (lines 11-23)
2. Inside the container run:

include('reconstructions.jl')