brainage/README.md

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 <singularity_file_path> \
                  -SAVE_ALL <yes/no> \
                  -CONTAINER_PATH <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 .sif image of the model

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> \