Merge pull request #70 from MELDProject/dev_docker

fix issue documentation singularity

Author: kwagstyl

README.md

@@ -3,6 +3,7 @@
 # MELD Graph 
 
 **Full documentation: [here](https://meld-graph.readthedocs.io/en/latest/index.html)**
+**Intro to MELD Graph and installation videos: [here](https://youtu.be/PIM1gwYNLns)**
 
 Graph based FCD lesion segmentation for the [MELD project](https://meldproject.github.io/).
 
@@ -44,7 +45,10 @@ The MELD surface-based graph FCD detection algorithm is intended for research pu
 You can install and use the MELD FCD prediction pipeline with :
 - [**docker container**](https://meld-graph.readthedocs.io/en/latest/install_docker.html) recommended for easy installation of the pipeline as all the prerequisite packages are already embedded into the container. Note: Dockers are not working on High Performance Computing (HCP) systems ; Not tested on Windows 
 - [**native installation**](https://meld-graph.readthedocs.io/en/latest/install_native.html) recommended for Mac and users that want to modify the code and/or use the code to train/test their own classifier. 
-- [**singularity container (Not tested yet)**](https://meld-graph.readthedocs.io/en/latest/install_singularity.html) enables to run a container on High Performance Computing (HCP) systems. 
+- [**singularity container (Not tested yet)**](https://meld-graph.readthedocs.io/en/latest/install_singularity.html) enables to run a container on High Performance Computing (HCP) systems.
+
+**YouTube tutorials available for the [docker installation](https://youtu.be/oduOe6NDXLA) and [native installation](https://youtu.be/jUCahJ-AebM)**
+
 
 ### Running the pipeline 
 Once installed you will be able to use the MELD FCD prediction pipeline on your data following the steps:
@@ -53,6 +57,8 @@ Once installed you will be able to use the MELD FCD prediction pipeline on your
 3. Run the prediction pipeline: [guidelines](https://meld-graph.readthedocs.io/en/latest/run_prediction_pipeline.html)
 4. Interpret the results: [guidelines](https://meld-graph.readthedocs.io/en/latest/interpret_results.html)
 
+**YouTube tutorials available to run the [harmonisation step](https://youtu.be/te_TR6sA5sQ), to run the [prediction pipeline](https://youtu.be/OZg1HSzqKyc) and to [interpret the pipeline results](https://youtu.be/dSyd1zOn4F8)**
+
 Note: If you have a question or if you are running into issues at any stage (installation/use/interpretation), have a look at our [FAQs](https://meld-graph.readthedocs.io/en/latest/FAQs.html) page to see if we have not already answered them. 
 
 **What is the harmonisation process ?**

docs/run_prediction_pipeline.md

@@ -53,6 +53,7 @@ Then run the command
 ./meldgraph.sh new_pt_pipeline.py -id <subject_id> 
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 
@@ -108,6 +109,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh new_pt_pipeline.py -id sub-001 --fastsurfer
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 ```bash
@@ -132,6 +134,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh new_pt_pipeline.py -id sub-001 -harmo_code H1
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 ```bash
@@ -156,6 +159,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh new_pt_pipeline.py -ids list_subjects.txt --parallelise
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 ```bash
@@ -195,6 +199,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh run_script_preprocessing.py -id sub-001
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 First you will need to mount the `meld_data` folder to the `/data` folder of the container by running:
@@ -224,6 +229,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh run_script_segmentation.py -h
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 ```bash
@@ -262,6 +268,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh run_script_preprocessing.py -id sub-001
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 First you will need to mount the `meld_data` folder to the `/data` folder of the container by running:
@@ -291,6 +298,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh run_script_preprocessing.py -h
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 ```bash
@@ -325,6 +333,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh run_script_prediction.py -id sub-001
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 First you will need to mount the `meld_data` folder to the `/data` folder of the container by running:
@@ -354,6 +363,7 @@ DOCKER_USER="$(id -u):$(id -g)" docker compose run meld_graph python scripts/new
 ./meldgraph.sh run_script_prediction.py -h
 ```
 
+:::
 :::{tab-item} Singularity
 :sync: singularity
 ```bash