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fetal2neonatal_stack_jd_for_randomise.py
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fetal2neonatal_stack_jd_for_randomise.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
stack all JD for fslrandomise, neonatal space symmetrical
"""
# IMPORT Libraries ------------------------------------------------
# %%
import os
import shutil
import sys
# %%
# Global variables -----------------------------
from config_fet2neo import subjects, bash_cmd
# %%
# Functions ----------------------------------------------------
def get_image_list_string(subjects):
string=''
subject_list=''
for subj in subjects:
string=" ".join([string, 'path'])
subject_list+=subj+' 1 \n'
for subj in subjects:
string=" ".join([string, 'path'])
subject_list+=str(subj)+' 0 \n'
return string, subject_list
def get_image_list_string_flipped_only(subjects):
string=''
subject_list=''
for subj in subjects:
string=" ".join([string, 'path'])
subject_list+=str(subj)+' 1 \n'
return string, subject_list
def stack_images(image_list_string, JD_merged_path):
bash_cmd('fslmerge -a '+JD_merged_path+' '+image_list_string )
#fslmerge -a JD_merged ${final_group}
# %%
image_string, subject_list = get_image_list_string(subjects)#
print(subject_list)
stack_images(image_string, 'outputpath.nii.gz')
image_string, subject_list = get_image_list_string_flipped_only(subjects)
stack_images(image_string, 'outputpath.nii.gz')