Talk:Automated Anatomical Labeling

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[edit] Check labeling

import re
import requests
from urllib import quote
url_rbb = " regions in AAL"
url_pages = ""
pattern_fields = re.compile(r'\s*\|\s*(\w+)\s*=\s*([^\|]*\w)', re.DOTALL | re.UNICODE)
pattern_brainregion = re.compile('{{brain region(\s*?\|.*?)}}', 
                                      re.DOTALL | re.IGNORECASE | re.UNICODE)
response = requests.get(url_rbb).json()
pagetitles = [page['title'] for page in response['query']['categorymembers']]
while 'query-continue' in response:
    url_continue = url_rbb + '&cmcontinue=' + response['query-continue']['categorymembers']['cmcontinue'].encode('utf-8')
    response = requests.get(url_continue).json()
    pagetitles.extend([page['title'] for page in response['query']['categorymembers']])
brainregions = []
for pagetitle in pagetitles:
    raw = unicode(requests.get(url_pages + quote(pagetitle.encode('utf-8'))).content, 'utf-8')
    print pagetitle 
    brainregion = pattern_brainregion.findall(raw)
    if brainregion:
# Show old AAL IDs (if any):
for brainregion in brainregions:
    if int(brainregion['aal']) < 1000:
# List the brain regions
for n, brainregion in enumerate(sorted(brainregions, key=lambda br: br['aal']), start=1):
    print("{:3} {:50} {}".format(n, brainregion['name'], brainregion['aal']))
# Are there any duplicates?
import collections
collections.Counter([br['aal'] for br in brainregions])
# Compare with text file in AAL distribution
from os.path import expanduser, join
filename = join(expanduser('~'), 'matlab', 'aal_for_SPM8', 'ROI_MNI_V4.txt')
aal = dict([line.split()[3:0:-1] for line in open(filename).readlines()])
for n, brainregion in enumerate(brainregions, start=1):
    print("{} {:22} {}".format(n, aal[brainregion['aal']], brainregion['name']))
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