def prepare_data(data_dir, output_dir, pipeline = "cpac", quality_checked = True):
# get dataset
print("Loading dataset...")
abide = datasets.fetch_abide_pcp(data_dir = data_dir,
pipeline = pipeline,
quality_checked = quality_checked)
# make list of filenames
fmri_filenames = abide.func_preproc
# load atlas
multiscale = datasets.fetch_atlas_basc_multiscale_2015()
atlas_filename = multiscale.scale064
# initialize masker object
masker = NiftiLabelsMasker(labels_img=atlas_filename,
standardize=True,
memory='nilearn_cache',
verbose=0)
# initialize correlation measure
correlation_measure = ConnectivityMeasure(kind='correlation', vectorize=True,
discard_diagonal=True)
try: # check if feature file already exists
# load features
feat_file = os.path.join(output_dir, 'ABIDE_BASC064_features.npz')
X_features = np.load(feat_file)['a']
print("Feature file found.")
except: # if not, extract features
X_features = [] # To contain upper half of matrix as 1d array
print("No feature file found. Extracting features...")
for i,sub in enumerate(fmri_filenames):
# extract the timeseries from the ROIs in the atlas
time_series = masker.fit_transform(sub)
# create a region x region correlation matrix
correlation_matrix = correlation_measure.fit_transform([time_series])[0]
# add to our container
X_features.append(correlation_matrix)
# keep track of status
print('finished extracting %s of %s'%(i+1,len(fmri_filenames)))
# Save features
np.savez_compressed(os.path.join(output_dir, 'ABIDE_BASC064_features'),
a = X_features)
# Dimensionality reduction of features with PCA
print("Running PCA...")
pca = PCA(0.99).fit(X_features) # keeping 99% of variance
X_features_pca = pca.transform(X_features)
# Transform phenotypic data into dataframe
abide_pheno = pd.DataFrame(abide.phenotypic)
# Get the target vector
y_target = abide_pheno['DX_GROUP']
return(X_features_pca, y_target)
def test_fetch_abide_pcp():
local_url = "file://" + datadir
ids = [('50%03d' % i).encode() for i in range(800)]
filenames = ['no_filename'] * 800
filenames[::2] = ['filename'] * 400
pheno = np.asarray(list(zip(ids, filenames)), dtype=[('subject_id', int),
('FILE_ID', 'U11')])
# pheno = pheno.T.view()
file_mock.add_csv('Phenotypic_V1_0b_preprocessed1.csv', pheno)
# All subjects
dataset = datasets.fetch_abide_pcp(data_dir=tmpdir, url=local_url,
quality_checked=False, verbose=0)
assert_equal(len(dataset.func_preproc), 400)
def test_fetch_abide_pcp():
local_url = "file://" + datadir
ids = [('50%03d' % i).encode() for i in range(800)]
filenames = ['no_filename'] * 800
filenames[::2] = ['filename'] * 400
pheno = np.asarray(list(zip(ids, filenames)),
dtype=[('subject_id', int), ('FILE_ID', 'U11')])
# pheno = pheno.T.view()
file_mock.add_csv('Phenotypic_V1_0b_preprocessed1.csv', pheno)
# All subjects
dataset = datasets.fetch_abide_pcp(data_dir=tmpdir,
url=local_url,
quality_checked=False,
verbose=0)
assert_equal(len(dataset.func_preproc), 400)
def get_dataset(dataset, max_images=np.inf, **kwargs):
"""Retrieve & normalize dataset from nilearn"""
# Download
if dataset == 'neurovault':
images, term_scores = fetch_neurovault(max_images=max_images, **kwargs)
elif dataset == 'abide':
dataset = datasets.fetch_abide_pcp(
n_subjects=min(94, max_images), **kwargs)
images = [{'absolute_path': p} for p in dataset['func_preproc']]
term_scores = None
elif dataset == 'nyu':
dataset = datasets.fetch_nyu_rest(
n_subjects=min(25, max_images), **kwargs)
images = [{'absolute_path': p} for p in dataset['func']]
term_scores = None
else:
raise ValueError("Unknown dataset: %s" % dataset)
return images, term_scores
def fetch_generated_data(data_dir, output_dir):
print("Loading dataset...")
abide = datasets.fetch_abide_pcp(data_dir=data_dir,
pipeline='cpac',
quality_checked=True)
feat_file = os.path.join(output_dir, 'ABIDE_BASC064_features.npz')
X_features = np.load(feat_file)['a']
feat_file_autism = os.path.join(output_dir, 'generated_data_asd_300.csv')
X_features_autism = pd.read_csv(feat_file_autism, sep=',', header=None, skiprows=1)
X_features_autism = X_features_autism.drop(X_features_autism.columns[0], axis=1)
feat_file_control = os.path.join(output_dir, 'generated_data_tc_300.csv')
X_features_control = pd.read_csv(feat_file_control, sep=',', header=None, skiprows=1)
X_features_control = X_features_control.drop(X_features_control.columns[0], axis=1)
X_features_all = np.vstack((X_features, X_features_autism.values, X_features_control.values))
print('Stacked synthetic and original features ', X_features_all.shape)
print("Running PCA...")
pca = PCA(0.99).fit(X_features_all) # keeping 99% of variance
X_features_pca = pca.transform(X_features_all)
# Transform phenotypic data into dataframe
abide_pheno = pd.DataFrame(abide.phenotypic)
# Get the target vector
y_target = abide_pheno['DX_GROUP']
# add dx_group for synthetic data
y_target_arr = np.append(y_target.values, np.ones(100)) # add asd group
y_target_arr = np.append(y_target_arr, np.zeros(100)) # add tc group
y_target = pd.Series(y_target_arr)
return (X_features_pca, y_target)
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Dec 9 20:03:28 2018
@author: xinyang
This program is to find out the top five correlatd and anti-correlated ROIs of ASD and TD
"""
from nilearn.datasets import fetch_abide_pcp
import pandas as pd
import numpy as np
labels = pd.read_csv('CC400_ROI_labels.csv')
atlas_filename = 'cc400_roi_atlas.nii.gz'
abide = fetch_abide_pcp(derivatives = ['rois_cc400'], pipeline = 'cpac', quality_checked = False)
y = abide.phenotypic['DX_GROUP']
names = ['DX_GROUP','rois_cc400']
data = pd.DataFrame([y,abide.rois_cc400]).transpose()
data.columns = names
ASD = data[data['DX_GROUP']==1]['rois_cc400'] #505
TD = data[data['DX_GROUP']==2]['rois_cc400'] #530
##############################################################################
# Compute and display a correlation matrix
# -----------------------------------------
# Plot the correlation matrix
from nilearn import plotting
from nilearn.connectome import ConnectivityMeasure
correlation_measure = ConnectivityMeasure(kind='correlation')
import gzip
import csv
import numpy as np
from nilearn.input_data import NiftiLabelsMasker
from nilearn import datasets
__author__ = '2d Lt Kyle Palko'
__version__ = 'v0.1'
pipe = 'cpac'
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test' # set where the data should be saved
# path = '/home/kap/Thesis/Data/DL'
# define the pipeline used to preprocess the data
derivative = 'rois_tt' # define what data should be pulled
datasets.fetch_abide_pcp(data_dir=path, pipeline=pipe, band_pass_filtering=True, global_signal_regression=True,
derivatives=[derivative])
# local variables and paths #
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/' # working directory
filt = 'filt_global'
stud = 'Test/ABIDE_pcp/{0}/{1}/'.format(pipe, filt) # location that download happened to
# stud = 'C200/ABIDE_pcp/{0}/{1}/'.format(pipe, filt)
# stud = '/ABIDE_pcp/{0}/{1}/'.format(pipe, filt)
# stud = 'Data/'
# lab = path + 'Label/' # location of CSV files for labeling
lab = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Data/'
# lab = '/home/kap/Thesis/Data/Label/'
mask_name = 'tt97_prep'
# build two lists of strings from CSV files to use to match the subjects and their diagnosis
idlab = [] # subject IDs
sys.path.append("../inverse_covariance")
from inverse_covariance import (
QuicGraphicalLasso,
QuicGraphicalLassoCV,
QuicGraphicalLassoEBIC,
AdaptiveGraphicalLasso,
)
plt.ion()
# Fetch the coordinates of power atlas
power = datasets.fetch_coords_power_2011()
coords = np.vstack((power.rois["x"], power.rois["y"], power.rois["z"])).T
# Loading the functional datasets
abide = datasets.fetch_abide_pcp(n_subjects=1)
abide.func = abide.func_preproc
# print basic information on the dataset
# 4D data
print("First subject functional nifti images (4D) are at: %s" % abide.func[0])
###############################################################################
# Masking: taking the signal in a sphere of radius 5mm around Power coords
masker = input_data.NiftiSpheresMasker(
seeds=coords,
smoothing_fwhm=4,
radius=5.,
standardize=True,
detrend=True,
from nilearn.datasets import fetch_abide_pcp
import pandas
import os
df = pandas.read_csv('Phenotypic_V1_0b_preprocessed1.csv', sep='\t')
site_id = np.unique(df['SITE_ID'])
print(site_id)
for S in (site_id):
data_dir = 'test'
#DX_GROUP: 1 is autism, 2 is control
abidedata_func_normal = fetch_abide_pcp(data_dir=data_dir,
n_subjects=None,
pipeline='cpac',
band_pass_filtering=True,
global_signal_regression=True,
derivatives=['func_preproc'],
quality_checked=True,
DX_GROUP=2,
SITE_ID=S)
abidedata_func_autism = fetch_abide_pcp(data_dir=data_dir,
n_subjects=None,
pipeline='cpac',
band_pass_filtering=True,
global_signal_regression=True,
derivatives=['func_preproc'],
quality_checked=True,
DX_GROUP=1,
SITE_ID=S)
print(len(abidedata_func_normal['func_preproc']))
import numpy as np
from nilearn.input_data import NiftiMapsMasker
from nilearn.regions import RegionExtractor
from nilearn.connectome import ConnectivityMeasure
import matplotlib.pyplot as plt
# In[ ]:
# for fetching dataset for first instance only
abide = datasets.fetch_abide_pcp(data_dir= data_dir2,derivatives=['func_preproc'],
SITE_ID=['NYU'],
# n_subjects=3
)
print(abide.keys())
func = abide.func_preproc
# In[ ]:
type(func)
# In[ ]:
import gzip
import numpy as np
import csv
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test' # set where the data should be saved
# sub_id = [50060] # sets the subject ids that should be pulled simple 3
# sub_id = range(50003, 50061) # calls all of the PITT study subjects
pipeline = 'cpac' # define the pipeline used to preprocess the data
derivative = 'func_preproc' # define what data should be pulled
# set the directory where the data is stored so the script can find and rename the data
os.chdir('/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test/ABIDE_pcp/cpac/filt_noglobal/')
for n in sub_id:
# download the fMRI image
datasets.fetch_abide_pcp(data_dir=path, n_subjects=1, pipeline=pipeline, band_pass_filtering=True,
derivatives=[derivative], SUB_ID=n) # fetch the data based on the subject ID
# extract and rename the image file
for name in glob.glob('*' + str(n) + '*.gz'): # use glob to find the recently download filename
inF = gzip.open(name, 'rb') # opens .gz file
outF = open('{0}.nii'.format(n), 'wb') # creates a new file using fileID as the name
outF.write(inF.read()) # extract and write the .nii file
inF.close()
outF.close()
os.remove(name) # deletes the .nii.gz file
# download the image's corresponding mask
# datasets.fetch_abide_pcp(data_dir=path, n_subjects=1, pipeline=pipeline, band_pass_filtering=True,
# derivatives=['func_mask'], SUB_ID=n)
# # extract and rename the mask
# for name in glob.glob('*' + str(n) + '*.gz'): # use glob to find the recently download filename
# inF = gzip.open(name, 'rb') # opens .gz file
# By default it used two classifiers, LinearSVC ('l1', 'l2') and Ridge
# Not so good documentation and implementation here according to me
learn_brain_regions.classify(labels, cv=[(train_index, test_index)],
scoring='roc_auc')
print(learn_brain_regions.scores_)
return learn_brain_regions
###########################################################################
# Data
# ----
# Load the datasets from Nilearn
from nilearn import datasets
abide_data = datasets.fetch_abide_pcp(pipeline='cpac')
func_imgs = abide_data.func_preproc
phenotypic = abide_data.phenotypic
# class type for each subject is different
class_type = 'DX_GROUP'
cache_path = 'data_processing_abide'
from sklearn.externals.joblib import Memory, Parallel, delayed
mem = Memory(cachedir=cache_path)
connectome_regress_confounds = None
from nilearn_utils import data_info
target_shape, target_affine, _ = data_info(func_imgs[0])
def main():
parser = argparse.ArgumentParser(
description=
'Download ABIDE data and compute functional connectivity matrices')
parser.add_argument(
'--pipeline',
default='cpac',
type=str,
help=
'Pipeline to preprocess ABIDE data. Available options are ccs, cpac, dparsf and niak.'
' default: cpac.')
parser.add_argument(
'--atlas',
default='cc200',
help=
'Brain parcellation atlas. Options: ho, cc200 and cc400, default: cc200.'
)
parser.add_argument(
'--download',
default=True,
type=str2bool,
help=
'Dowload data or just compute functional connectivity. default: True')
args = parser.parse_args()
print(args)
params = dict()
pipeline = args.pipeline
atlas = args.atlas
download = args.download
# Files to fetch
files = ['rois_' + atlas]
filemapping = {
'func_preproc': 'func_preproc.nii.gz',
files[0]: files[0] + '.1D'
}
# Download database files
if download == True:
abide = datasets.fetch_abide_pcp(data_dir=root_folder,
pipeline=pipeline,
band_pass_filtering=True,
global_signal_regression=False,
derivatives=files,
quality_checked=False)
subject_IDs = Reader.get_ids() #changed path to data path
subject_IDs = subject_IDs.tolist()
# Create a folder for each subject
for s, fname in zip(subject_IDs,
Reader.fetch_filenames(subject_IDs, files[0], atlas)):
subject_folder = os.path.join(data_folder, s)
if not os.path.exists(subject_folder):
os.mkdir(subject_folder)
# Get the base filename for each subject
base = fname.split(files[0])[0]
# Move each subject file to the subject folder
for fl in files:
if not os.path.exists(
os.path.join(subject_folder, base + filemapping[fl])):
shutil.move(base + filemapping[fl], subject_folder)
time_series = Reader.get_timeseries(subject_IDs, atlas)
# Compute and save connectivity matrices
Reader.subject_connectivity(time_series, subject_IDs, atlas, 'correlation')
Reader.subject_connectivity(time_series, subject_IDs, atlas,
'partial correlation')
__author__ = '2d Lt Kyle Palko' from nilearn import datasets import time start = time.time() path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test' # set where the data should be saved pipeline = 'cpac' # define the pipeline used to preprocess the data derivative = 'func_preproc' # define what data should be pulled stud = '/ABIDE_pcp/cpac/filt_noglobal/e806a9ef657f316b760441d3649f7cb6' datasets.fetch_abide_pcp(data_dir=path, pipeline=pipeline, band_pass_filtering=True, derivatives=[derivative])
num_subjects = 871 # Number of subjects
root_folder = '/path/to/data/'
data_folder = os.path.join(root_folder, 'ABIDE_pcp/cpac/filt_noglobal')
# Files to fetch
files = ['rois_ho']
filemapping = {'func_preproc': 'func_preproc.nii.gz', 'rois_ho': 'rois_ho.1D'}
shutil.copyfile('./subject_IDs.txt',
os.path.join(data_folder, 'subject_IDs.txt'))
# Download database files
abide = datasets.fetch_abide_pcp(data_dir=root_folder,
n_subjects=num_subjects,
pipeline=pipeline,
band_pass_filtering=True,
global_signal_regression=False,
derivatives=files)
subject_IDs = Reader.get_ids(num_subjects)
subject_IDs = subject_IDs.tolist()
# Create a folder for each subject
for s, fname in zip(subject_IDs, Reader.fetch_filenames(subject_IDs,
files[0])):
subject_folder = os.path.join(data_folder, s)
if not os.path.exists(subject_folder):
os.mkdir(subject_folder)
# Get the base filename for each subject
base = fname.split(files[0])[0]
# sub_id = [50060] # sets the subject ids that should be pulled simple 3
# sub_id = range(50003, 50061) # calls all of the PITT study subjects
pipeline = 'cpac' # define the pipeline used to preprocess the data
derivative = 'func_preproc' # define what data should be pulled
# set the directory where the data is stored so the script can find and rename the data
os.chdir(
'/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test/ABIDE_pcp/cpac/filt_noglobal/'
)
for n in sub_id:
# download the fMRI image
datasets.fetch_abide_pcp(
data_dir=path,
n_subjects=1,
pipeline=pipeline,
band_pass_filtering=True,
derivatives=[derivative],
SUB_ID=n) # fetch the data based on the subject ID
# extract and rename the image file
for name in glob.glob(
'*' + str(n) +
'*.gz'): # use glob to find the recently download filename
inF = gzip.open(name, 'rb') # opens .gz file
outF = open('{0}.nii'.format(n),
'wb') # creates a new file using fileID as the name
outF.write(inF.read()) # extract and write the .nii file
inF.close()
outF.close()
os.remove(name) # deletes the .nii.gz file
import numpy as np
from nilearn.input_data import NiftiLabelsMasker
from nilearn import datasets
__author__ = '2d Lt Kyle Palko'
__version__ = 'v0.1'
pipe = 'cpac'
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test' # set where the data should be saved
# path = '/home/kap/Thesis/Data/DL'
# define the pipeline used to preprocess the data
derivative = 'rois_tt' # define what data should be pulled
datasets.fetch_abide_pcp(data_dir=path,
pipeline=pipe,
band_pass_filtering=True,
global_signal_regression=True,
derivatives=[derivative])
# local variables and paths #
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/' # working directory
filt = 'filt_global'
stud = 'Test/ABIDE_pcp/{0}/{1}/'.format(
pipe, filt) # location that download happened to
# stud = 'C200/ABIDE_pcp/{0}/{1}/'.format(pipe, filt)
# stud = '/ABIDE_pcp/{0}/{1}/'.format(pipe, filt)
# stud = 'Data/'
# lab = path + 'Label/' # location of CSV files for labeling
lab = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Data/'
# lab = '/home/kap/Thesis/Data/Label/'
mask_name = 'tt97_prep'
from matplotlib import pyplot as plt
# Plot the atlas. Different Atlases provide different regions of interest (ROIs). Some ROIs are larger than others. The
# TT and AAL atlases are much smaller than the CC400. These atlases must be downloaded beforehand from
# https://preprocessed-connectomes-project.github.io/abide/Pipelines.html#regions_of_interest
pltt.plot_roi('tt_mask_pad.nii', output_file='tt_roi_plot')
pltt.plot_roi('aal_mask_pad.nii', output_file='aal_roi_plot')
pltt.plot_roi('CC400.nii', output_file='cc400_roi_plot')
print('Completed brain ROI Images')
# download the data (only two images in this case)
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test' # set where the data should be saved
ab_img_one = datasets.fetch_abide_pcp(data_dir=path,
n_subjects=1,
pipeline='cpac',
band_pass_filtering=True,
derivatives=['func_preproc'],
SUB_ID=[50003])
ab_img_two = datasets.fetch_abide_pcp(data_dir=path,
n_subjects=1,
pipeline='cpac',
band_pass_filtering=True,
derivatives=['func_preproc'],
SUB_ID=[50004])
ab_mask_one = datasets.fetch_abide_pcp(data_dir=path,
n_subjects=1,
pipeline='cpac',
band_pass_filtering=True,
derivatives=['func_mask'],
SUB_ID=[50003])
from nilearn import datasets
from nilearn import plotting as pltt
from matplotlib import pyplot as plt
# Plot the atlas. Different Atlases provide different regions of interest (ROIs). Some ROIs are larger than others. The
# TT and AAL atlases are much smaller than the CC400. These atlases must be downloaded beforehand from
# https://preprocessed-connectomes-project.github.io/abide/Pipelines.html#regions_of_interest
pltt.plot_roi('tt_mask_pad.nii', output_file='tt_roi_plot')
pltt.plot_roi('aal_mask_pad.nii', output_file='aal_roi_plot')
pltt.plot_roi('CC400.nii', output_file='cc400_roi_plot')
print('Completed brain ROI Images')
# download the data (only two images in this case)
path = '/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/Test' # set where the data should be saved
ab_img_one = datasets.fetch_abide_pcp(data_dir=path, n_subjects=1, pipeline='cpac', band_pass_filtering=True,
derivatives=['func_preproc'], SUB_ID=[50003])
ab_img_two = datasets.fetch_abide_pcp(data_dir=path, n_subjects=1, pipeline='cpac', band_pass_filtering=True,
derivatives=['func_preproc'], SUB_ID=[50004])
ab_mask_one = datasets.fetch_abide_pcp(data_dir=path, n_subjects=1, pipeline='cpac', band_pass_filtering=True,
derivatives=['func_mask'], SUB_ID=[50003])
ab_mask_two = datasets.fetch_abide_pcp(data_dir=path, n_subjects=1, pipeline='cpac', band_pass_filtering=True,
derivatives=['func_mask'], SUB_ID=[50003])
my_data = ['pitt3.nii', 'pitt4.nii'] # have to rename the two files that were downloaded
# apply mask to the fMRI images. The mask is the regions of the image that will be extracted for use.
from nilearn.masking import apply_mask
masked_data = apply_mask(my_data[0], 'pitt3mask.nii') # just mask the first image (fMRI, mask)
print('Completed Masking')