brainage
get_brainage.sh
This script is used for brain age prediction. Below is a description of each input arguments:
Usage
./get_brainage.sh -input <input_directory> \
-output <output_directory> \
-BIDS <yes/no> \
-CONDOR <yes/no> \
-RAW <yes/no> \
-RUN_FILE <bash_file_path> \
-SAVE_ALL <yes/no> \
-CONTAINER_PATH <directory_path> \
- input: input directory (can be a folder containing raw or preprocessed T1 MR Image which can be .nii, .nii.gz or .mgz)
- output: output directory where the results will be stored in
<subject_name>_<model>.csv
- BIDS: are the input files stored in BIDS format ?
- CONDOR: provides a
condor.submit file
- RAW: are the input files raw ?
- RUN_FILE: path to the
run_<model>.sh file
- SAVE_ALL: Do you want to save the intermidiate files (for ex:
subject_features), if yes then the files will be stored in the folder <subject_name>_<model>
- CONTAINER_PATH: path to the directory containing the container images
brainageR folder:
1) Building the container
singularity build brainageR.sif brainageR.def (not working at the moment)
2) Run the get_brainage.sh with the proper files and paths
Example:
./get_brainage.sh -input <input_directory> \
-output <output_directory> \
-BIDS <yes/no> \
-CONDOR <yes/no> \
-RAW <yes/no> \
-RUN_FILE run_brainageR.sh \
-SAVE_ALL <yes/no> \
-CONTAINER_PATH <path/to/brainageR.sif> \
Enigma folder:
1) Building the containers
Preprocessing: singularity build --fakeroot cat_preprocessing.simg Singularity_r2042
Prediction: singularity build --fakeroot enigma_stacking_agepred.simg enigma_stacking_pred.def
/!\ It is important to not change the name of the containers
2) Run the get_brainage.sh with the proper files and paths
Example:
./get_brainage.sh -input <input_directory> \
-output <output_directory> \
-BIDS <yes/no> \
-CONDOR <yes/no> \
-RAW <yes/no> \
-RUN_FILE run_enigma.sh \
-SAVE_ALL <yes/no> \
-CONTAINER_PATH <path/to/brainageR.sif> \
