Update 'README.md'

README.md

@@ -14,7 +14,7 @@ This script is used for brain age prediction. Below is a description of each inp
                   -RAW <yes/no> \
                   -RUN_FILE <bash_file_path> \
                   -SAVE_ALL <yes/no> \
-                  -CONTAINER_PATH <directory_path> \
+                  -CONTAINER_PATH <path/to/containers> \
 ```
 
 * input: input directory (can be a folder containing raw or preprocessed T1 MR Image which can be .nii, .nii.gz or .mgz)
@@ -44,7 +44,7 @@ Example:
                   -RAW <yes/no> \
                   -RUN_FILE run_brainageR.sh \
                   -SAVE_ALL <yes/no> \
-                  -CONTAINER_PATH <path/to/brainageR.sif> \
+                  -CONTAINER_PATH <path/to/containers> \
 ```
 
 ### Enigma folder:
@@ -69,5 +69,39 @@ Example:
                   -RAW <yes/no> \
                   -RUN_FILE run_enigma.sh \
                   -SAVE_ALL <yes/no> \
-                  -CONTAINER_PATH <path/to/brainageR.sif> \
+                  -CONTAINER_PATH <path/to/containers> \
 ```
+
+### More folder:
+
+1) Building the containers
+
+Preprocessing: `singularity build --fakeroot cat_preprocessing.simg Singularity_r2042` 
+
+Prediction: `singularity build --fakeroot BA_predict.sif BA_predict.recipe `
+
+/!\ It is important to not change the name of the containers
+
+2) Run the `get_brainage.sh` with the proper files and paths
+
+Examples:
+
+**For one subject**:
+
+
+
+
+
+```
+./get_brainage.sh -input <input_directory> \
+                  -output <output_directory> \
+                  -BIDS <yes/no> \
+                  -CONDOR <yes/no> \
+                  -RAW <yes/no> \
+                  -RUN_FILE run_more.sh \
+                  -SAVE_ALL <yes/no> \
+                  -CONTAINER_PATH <path/to/containers> \
+                  -MODEL_NAME <model_name>
+```
+
+