In [1]:
import common
reload(common)
importing IPython notebook from common.ipynb
importing IPython notebook from common.ipynb
Out[1]:
<module 'common' from 'common.ipynb'>
In [2]:
import os
from datetime import datetime
import numpy as np
import pandas as pd
pd.set_option('display.max_rows', 25)
pd.set_option('display.max_columns', 50)
In [3]:
full = np.zeros((148, 148, len(common.subject_list)))
for i, subject in enumerate(common.subject_list):
scdir = common.sc_dir(subject)
conn, processed_seed_list, N = common.single_process(scdir)
full[:, :, i] = conn
Define the "English->Freesufer" mapping.
In [4]:
rois_of_interest = {'BA44': 'G_front_inf-Opercular',
'AG': 'G_pariet_inf-Angular',
'MTG': 'G_temporal_middle',
'BA45': 'G_front_inf-Triangul',
'BA47': 'S_orbital_lateral', # or G_orbital?
}
For each hemisphere:
processed_seed_list.full.seed == target):full.data[column_name].
In [5]:
data = {}
for hemi in ('lh', 'rh'):
for seed_name, seed_label in rois_of_interest.items():
seed = '{}.{}'.format(hemi, seed_label)
seed_index = processed_seed_list.index(seed)
for target_name, target_label in rois_of_interest.items():
if seed_name == target_name:
continue
target = '{}.{}'.format(hemi, target_label)
column_temp = "{hemi}.{seed_name}-{hemi}.{target_name}"
column_name = column_temp.format(hemi=hemi,
seed_name=seed_name,
target_name=target_name)
target_index = processed_seed_list.index(target)
data[column_name] = full[seed_index, target_index, :]
Make a dataframe out of the data, using the subject list as the index.
In [6]:
df = pd.DataFrame(data, index=common.subject_list)
# sanity check
ag_index = processed_seed_list.index('lh.G_pariet_inf-Angular')
mtg_index = processed_seed_list.index('lh.G_temporal_middle')
assert df['lh.AG-lh.MTG']['061_206924'] == full[ag_index, mtg_index, 0]
df
Out[6]:
lh.AG-lh.BA44
lh.AG-lh.BA45
lh.AG-lh.BA47
lh.AG-lh.MTG
lh.BA44-lh.AG
lh.BA44-lh.BA45
lh.BA44-lh.BA47
lh.BA44-lh.MTG
lh.BA45-lh.AG
lh.BA45-lh.BA44
lh.BA45-lh.BA47
lh.BA45-lh.MTG
lh.BA47-lh.AG
lh.BA47-lh.BA44
lh.BA47-lh.BA45
lh.BA47-lh.MTG
lh.MTG-lh.AG
lh.MTG-lh.BA44
lh.MTG-lh.BA45
lh.MTG-lh.BA47
rh.AG-rh.BA44
rh.AG-rh.BA45
rh.AG-rh.BA47
rh.AG-rh.MTG
rh.BA44-rh.AG
rh.BA44-rh.BA45
rh.BA44-rh.BA47
rh.BA44-rh.MTG
rh.BA45-rh.AG
rh.BA45-rh.BA44
rh.BA45-rh.BA47
rh.BA45-rh.MTG
rh.BA47-rh.AG
rh.BA47-rh.BA44
rh.BA47-rh.BA45
rh.BA47-rh.MTG
rh.MTG-rh.AG
rh.MTG-rh.BA44
rh.MTG-rh.BA45
rh.MTG-rh.BA47
061_206924
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Connect to redcap and join the databases?
Content source: VUIIS/tractography-notebooks
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