8.5.9. Understanding NiftiMasker and mask computation

In this example, the Nifti masker is used to automatically compute a mask.

For data that has already been masked, the default strategy works out of the box.

However, for raw EPI, as in resting-state time series, we need to use the ‘epi’ strategy of the NiftiMasker.

In addition, we show here how to tweak the different parameters of the underlying mask extraction routine nilearn.masking.compute_epi_mask.

From already masked data

from nilearn.input_data import NiftiMasker
import nilearn.image as image
from nilearn.plotting import plot_roi, show

# Load Miyawaki dataset
from nilearn import datasets
miyawaki_dataset = datasets.fetch_miyawaki2008()

# print basic information on the dataset
print('First functional nifti image (4D) is located at: %s' %
      miyawaki_dataset.func[0])  # 4D data

miyawaki_filename = miyawaki_dataset.func[0]
miyawaki_mean_img = image.mean_img(miyawaki_filename)

# This time, we can use the NiftiMasker without changing the default mask
# strategy, as the data has already been masked, and thus lies on a
# homogeneous background

masker = NiftiMasker()

plot_roi(masker.mask_img_, miyawaki_mean_img,
         title="Mask from already masked data")


First functional nifti image (4D) is located at: /home/kamalakar/nilearn_data/miyawaki2008/func/data_figure_run01.nii.gz

From raw EPI data

# Load ADHD resting-state dataset
dataset = datasets.fetch_adhd(n_subjects=1)
epi_filename = dataset.func[0]

# Restrict to 100 frames to speed up computation
from nilearn.image import index_img
epi_img = index_img(epi_filename, slice(0, 100))

# To display the background
mean_img = image.mean_img(epi_img)

# Simple mask extraction from EPI images
# We need to specify an 'epi' mask_strategy, as this is raw EPI data
masker = NiftiMasker(mask_strategy='epi')
plot_roi(masker.mask_img_, mean_img, title='EPI automatic mask')

# Generate mask with strong opening
masker = NiftiMasker(mask_strategy='epi', mask_args=dict(opening=10))
plot_roi(masker.mask_img_, mean_img, title='EPI Mask with strong opening')

# Generate mask with a high lower cutoff
masker = NiftiMasker(mask_strategy='epi',
                     mask_args=dict(upper_cutoff=.9, lower_cutoff=.8,
plot_roi(masker.mask_img_, mean_img,
         title='EPI Mask: high lower_cutoff')
  • ../../_images/sphx_glr_plot_mask_computation_002.png
  • ../../_images/sphx_glr_plot_mask_computation_003.png
  • ../../_images/sphx_glr_plot_mask_computation_004.png

Extract time series

# trended vs detrended
trended = NiftiMasker(mask_strategy='epi')
detrended = NiftiMasker(mask_strategy='epi', detrend=True)
trended_data = trended.fit_transform(epi_img)
detrended_data = detrended.fit_transform(epi_img)

# The timeseries are numpy arrays, so we can manipulate them with numpy
import numpy as np

print("Trended: mean %.2f, std %.2f" %
      (np.mean(trended_data), np.std(trended_data)))
print("Detrended: mean %.2f, std %.2f" %
      (np.mean(detrended_data), np.std(detrended_data)))



Trended: mean 9649.84, std 2132.18
Detrended: mean 0.00, std 139.16

Total running time of the script: ( 0 minutes 5.193 seconds)

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