AAL atlas. Remove cerebellum ROIs and order left-right non consecutively

AAL_2_AALordered.txt

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb  5 16:37:53 2018

@author: asier
"""
import numpy as np
import nibabel as nib

atlas_old = '/home/asier/Desktop/aal/AAL.nii'
atlas_new = '/home/asier/Desktop/aal/AALnew.nii'

atlas_old_img = nib.load(atlas_old)

atlas_old_data = nib.load(atlas_old).get_data()
atlas_old_data_rois = np.unique(atlas_old_data)

for i, roi in enumerate(atlas_old_data_rois):
    if i ==0:
        pass
    else:
        if i <= 90:
            atlas_old_data[np.where(atlas_old_data==roi)]=i
        else:
            atlas_old_data[np.where(atlas_old_data==roi)]=0
        
        
atlas_new_data = np.zeros(atlas_old_data.shape)

counter = 1
for roi in range(1,91):
    if (roi % 2) == 1:
        atlas_new_data[np.where(atlas_old_data==roi)]=counter                    
    else:
        atlas_new_data[np.where(atlas_old_data==roi)]=counter+45
        counter += 1


atlas_new_data_img_corrected = nib.Nifti1Image(atlas_new_data,
                                               affine=atlas_old_img.affine)

nib.save(atlas_new_data_img_corrected,
         atlas_new)