example_code.py

# -*- coding: utf-8 -*-
"""
Created on Tue Dec  2 11:46:45 2025

@author: nicol
"""

import sys
import json

def get_name(tck_file:str,out_file:str):
    
    a_dict={} # create empty dictionary
    a_dict['tck_file']=tck_file # Example: '/data/subjects/SUBJ001/dMRI/tractography/SUBJ001_tractogram.tck'
    
    with open('data.json', 'w') as out_file:
        json.dump(a_dict, out_file)
    
    return

if __name__=='__main__':
    
    # Get input and output root + subject_id
    root_in = sys.argv[1] 
    root_out = sys.argv[2]
    sub = sys.argv[3]
    
    # Easily modify filepaths and dataset architecture
    tck_filepath=root_in+'subjects/'+sub+'/dMRI/tractography/'+sub+'_tractogram.tck' 
    # out_filepath=root_out+'subjects/'+sub+'/mri_modality/model/'+sub+'_model_edited.nii.gz'
    out_filepath=root_out+sub+'.json'

    get_name(tck_filepath,out_filepath)