From 8d71caed19d4911c9c9186bed735009fb4748f3e Mon Sep 17 00:00:00 2001
From: Korbinian Eckstein <korbinian.eckstein@gmail.com>
Date: Thu, 28 Sep 2023 17:52:27 +1000
Subject: [PATCH] pull mrsi scripts

---
 recipes/mrsiproc/README.md | 55 +++++---------------------------------
 recipes/mrsiproc/build.sh  |  5 +++-
 2 files changed, 11 insertions(+), 49 deletions(-)

diff --git a/recipes/mrsiproc/README.md b/recipes/mrsiproc/README.md
index 7702a72c..177beb3b 100644
--- a/recipes/mrsiproc/README.md
+++ b/recipes/mrsiproc/README.md
@@ -1,6 +1,6 @@
 
 ----------------------------------
-## mrsiproc/toolVersion ##
+## mrsiproc/0.0.1 ##
 
 Includes the following:  
 ##### -- OS: Ubuntu 20.04 (Built from fsl neurodocker)
@@ -9,67 +9,26 @@ Includes the following:
 ##### -- HD-BET           (Version 1.0)
 ##### -- LCModel 					(Version 6.3.1)
 ##### -- dcm2niix
-##### -- Python           (Version 3.10)
+##### -- Python           (Version 3.11.4)
 ##### -- Julia            (Version 1.9.3)
 
 
 Overview
 --------------------------------------------
-In its current stage, the container provides the environment, but the scripts need to be obtained separately.
+The MRSI reconstruction algorithms and scripts were created by the Wolfgang Bogner group.
 
-Setup
+To run applications outside of this container
 ---------------------------------------------
-  ### Start neuredesktop with a fixed mac-address
-  Add the option `--mac-address 02:42:ac:11:00:02` to the docker command used for starting Neurodesk (see https://www.neurodesk.org/docs/neurodesk/getting-started/).  
-  This ensures that the license can still be used after rebooting Neurodesk.   
-  Example for the Linux command to start Neurodesk:
-  ```bash
-  sudo docker run \
-  --shm-size=1gb -it --privileged --name neurodesktop \
-  --mac-address 02:42:ac:11:00:02 \
-  -v ~/neurodesktop-storage:/neurodesktop-storage \
-  -e HOST_UID="$(id -u)" -e HOST_GID="$(id -g)"\
-  -p 8080:8080 \
-  -h neurodesktop-20220813 vnmd/neurodesktop:20220813
-  ```
-  (The mac address can be different from the one used here, but it must match the one used as host name for activating the matlab license)
+  ml mrsiproc/0.0.1
 
-  ### MRSI Scripts
-  This container does not contain scripts for mrsi processing yet.  
-  They need to be stored under `neurodesktop-storage` and the path set in `InstallProgramPaths.sh`
 
-  ### MATLAB license
-  The MATLAB license can be obtained from https://au.mathworks.com/licensecenter
-  - Log in with your account  
-  - Click on the license number
-  - Select the tab "Install and Activate"
-  - In "Related Tasks" click on "Activate to Retrieve License File"
-  - Click "Activate a Computer"
-  - Enter the Information:  
-    Release: R2021b  
-    Operating System: Linux  
-    Host ID: 02:42:ac:11:00:02  
-    Computer Login Name: root
-  - When it says 'is the software installed', select yes
-  - Then select 'download license'
-  - Store the license under /neurodesktop-storage/license_matlab.lic  
-  
 Run MRSI scripts
 -----------------------------------------
-Run the scripts from within a singularity shell inside Neurodesk. Example:
-```bash
-singularity shell singularity shell /cvmfs/neurodesk.ardc.edu.au/containers/mrsiproc_toolVersion_20221026/mrsiproc_toolVersion_20221026.simg
-```
 ```bash
-Singularity> cd /neurodesktop-storage/mrsi_proc
-Singularity> ./Run_MRSI_test.sh
+bash Part1_ProcessMRSI.sh
+bash Part2_EvaluateMRSI.sh
 ```
 
-To run applications outside of this container
----------------------------------------------
-  (This is not working yet)  
-  ml mrsiproc/toolVersion
-
 Citation
 --------
   
diff --git a/recipes/mrsiproc/build.sh b/recipes/mrsiproc/build.sh
index 9c60be10..4aa68bbf 100755
--- a/recipes/mrsiproc/build.sh
+++ b/recipes/mrsiproc/build.sh
@@ -120,7 +120,10 @@ neurodocker generate ${neurodocker_buildMode} \
    --run="julia install_packages.jl" \
    --env JULIA_DEPOT_PATH="~/.julia:/opt/julia_depot" \
    \
-   --env DEPLOY_BINS="julia:python:dcm2niix:hd-bet:lcmodel:nii2mnc:bet:fsl" \
+   --workdir /opt `# Add MRSI pipeline scripts` \
+   --run="git clone https://github.com/korbinian90/mrsi_pipeline_neurodesk.git" \
+   --env PATH="\${PATH}:/opt/mrsi_pipeline_neurodesk/Part1:/opt/mrsi_pipeline_neurodesk/Part2" \
+   --env DEPLOY_BINS="julia:python:dcm2niix:hd-bet:lcmodel:nii2mnc:bet:fsl:fslmaths:Part1_ProcessMRSI.sh:Part2_EvaluateMRSI.sh" \
    \
    --copy README.md /README.md                          `# include README file in container` \
    \