getPicsOfHippo.py

import os
import pandas as pd
from datetime import datetime

SCRIPT_DIR = os.path.abspath(os.path.dirname(__file__))
FSL_DIR = os.path.join(SCRIPT_DIR, 'fsl')
RFA = os.path.join(FSL_DIR, 'bin', 'run_first_all')
OUTPUT_DIR = os.path.join(SCRIPT_DIR, 'output')

paths = pd.read_csv(os.path.join(SCRIPT_DIR, 'mriimg_meta_v5.csv'))['bids_path']

limit = int(os.environ['BS_LIMIT'])
if limit is not None:
    paths = paths[:limit]

for path in paths:
    parts = os.path.basename(path).replace('.nii.gz', '').split('_')
    patient_id = parts[0].replace('sub-ADNI', '')
    viscode = parts[1].replace('ses-', '').lower()
    output_dir = os.path.join(OUTPUT_DIR, patient_id, viscode)

    os.makedirs(output_dir, exist_ok=True)
    os.chdir(output_dir)
    prefix = f'{patient_id}-{viscode}'
    cmd = f'{RFA} -i {path} -o {prefix} -s L_Hipp,R_Hipp'
    print(f"Executing '{cmd}' from dir {output_dir}")
    os.system(cmd)

now = datetime.now()
current_time = now.strftime("%H:%M:%S")
print(f"We did it!\nFinished at: {current_time}")