|
|
@@ -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>
|
|
|
+```
|
|
|
+
|
|
|
+
|
