Merge pull request #44 from MELDProject/dev_docker

Dev docker

docs/FAQs.md

@@ -1,3 +1,31 @@
 # FAQs
 
-Coming soon!
+## Issues with native installation
+TBC
+
+## Issues with Docker installation
+TBC
+
+## Issues with Singularity/Apptainer installation
+
+---
+### Issue of space when with creating the SIF
+```bash
+INFO:    Creating SIF file... 
+FATAL:   While performing build: while creating squashfs: create command failed: exit status 1:  
+Write failed because No space left on device 
+```
+It means there is not enough space where the default singularity/apptainer cache and temporary directories are located. Usually the default cache is located in `$HOME/.singularity/cache` and the default temporary directory `$HOME/.tmp`\
+Solution:
+- You can make space in the default `$HOME` directory
+- You can change the singularity/apptainer cache and temporary directories for a folder where there is space:
+    ```bash
+    export SINGULARITY_CACHEDIR=<path_folder_with_space> 
+    export SINGULARITY_TMPDIR=<path_folder_with_space>
+    ```
+    Or with apptainer
+    ```bash
+    export APPTAINER_CACHEDIR=<path_folder_with_space> 
+    export APPTAINER_TMPDIR=<path_folder_with_space>
+    ```
+---

docs/install_singularity.md

@@ -10,18 +10,18 @@ Notes:
 ## Prerequisites
 
 ### Install Singularity
-You will need to have Singularity installed. Most of the HPC will already have Singularity installed. You can check if singularity is installed on your computer by running:
+You will need to have Singularity installed. Most of the HPC will already have Singularity installed or Apptainer. You can check if Singularity/Apptainer is installed on your computer by running:
 ```bash
 singularity --version
 ```
-If this command displays the singularity or apptainer version then it is already installed. If not, please follow the [guidelines](https://docs.sylabs.io/guides/3.0/user-guide/installation.html) to install singularity on your machine.
+If this command displays the singularity or apptainer version already installed. If not, please follow the [guidelines](https://docs.sylabs.io/guides/3.0/user-guide/installation.html) to install singularity on your machine.
 
 
 ## Freesurfer licence
 You will need to download a Freesurfer license.txt to enable Freesurfer/Fastsurfer to perform the segmentation. Please follow the [guidelines](https://surfer.nmr.mgh.harvard.edu/fswiki/License) to download the file and keep a record of the path where you saved it. 
 
 ## Configuration
-In order to run the singularity image, you'll need to  Build the singularity image from the meld_graph docker image. This will create a singularity image called meld_graph.sif where you ran the command. 
+In order to run the singularity image, you'll need to build the singularity image from the meld_graph docker image. This will create a singularity image called meld_graph.sif where you ran the command. 
 
 Make sure you have 20GB of storage space available for the docker
 
@@ -41,7 +41,10 @@ Before being able to use the classifier on your data, data paths need to be set
 export SINGULARITY_BINDPATH=/<path_to_meld_data_folder>:/data,<path_to_FS_license>/license.txt:/license.txt:ro
 export SINGULARITYENV_FS_LICENSE=/license.txt
 ```
-
+OR with Apptainer
+```bash
+export APPTAINER_BINDPATH=/<path_to_meld_data_folder>:/data,<path_to_FS_license>/license.txt:/license.txt:ro
+export APPTAINERENV_FS_LICENSE=/license.txt
 3. Run this command to download the data folder 
 
 ```bash

scripts/manage_results/plot_prediction_report.py

@@ -598,7 +598,7 @@ def generate_prediction_report(
                 ax4 = fig3.add_subplot(gs3[1])
                 display4 = plotting.plot_anat(
                     t1_file, colorbar=False, cut_coords=coords, 
-                    draw_cross=False, radiological=True, annotate=False,
+                    draw_cross=False, radiological=True, annotate=True,
                     figure=fig3, axes=ax4, vmax=vmax
                 )