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add missing import package
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notebooks/7_twolevel_glm_nilearn.md

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@@ -51,6 +51,7 @@ import datalad.api as dl
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import numpy as np
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import pandas as pd
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import nibabel as nib
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from scipy.stats import norm
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from nilearn.interfaces.fmriprep import load_confounds_strategy
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from nilearn.image import load_img, get_data, math_img, threshold_img
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from nilearn.glm.first_level import make_first_level_design_matrix, FirstLevelModel
@@ -500,6 +501,7 @@ def secondlevel_estimation(firstlevel_stats_list, design_matrix, firstlevel_cont
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stats['z_score'].to_filename(z_image_path)
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plot_path = os.path.join(workflow_out_dir, 'secondlevel_unthresholded_contrast-%s_zmap.jpg' % contrast_id)
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plot_glass_brain(stats['z_score'],
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colorbar=True,
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threshold=norm.isf(0.001),
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title='Unthresholded z map',
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output_file=plot_path)

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