pybraincompare.report package
Submodules
pybraincompare.report.animate module
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pybraincompare.report.animate.
animate_figure
()[source]
pybraincompare.report.colors module
colors.py: part of pybraincompare package
Color stuffs
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pybraincompare.report.colors.
get_colors
(N, color_format='decimal')[source]
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pybraincompare.report.colors.
peterson_roi_labels
(colors=True)[source]
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pybraincompare.report.colors.
random_colors
(N)[source]
pybraincompare.report.histogram module
histogram.py: part of pybraincompare package
Functions for histograms
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pybraincompare.report.histogram.
get_histogram_data
(data, width=12, height=4, color=None, ylabel='frequency', xlabel='map intensity value bins', title='Histogram of Intensity Values for Image', bins=25, remove_zeros=True)[source]
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pybraincompare.report.histogram.
histogram_image
(masked_data, remove_zero=False, title=None, line_value=None, xlabel=None, width=11, height=4, png_img_file=None, threshold=0.001)[source]
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pybraincompare.report.histogram.
plot_histogram
(image, title='Image Histogram', height=400, width=1000, view_in_browser=True, bins=25, remove_zeros=True)[source]
pybraincompare.report.image module
image.py: part of pybraincompare package
Functions for static images
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pybraincompare.report.image.
make_anat_image
(nifti_file, png_img_file=None)[source]
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pybraincompare.report.image.
make_glassbrain_image
(nifti_file, png_img_file=None)[source]
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pybraincompare.report.image.
make_roi_image
(nifti_file, png_img_file=None)[source]
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pybraincompare.report.image.
make_stat_image
(nifti_file, png_img_file=None)[source]
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pybraincompare.report.image.
plot_vline
(cur_val, label, ax)[source]
pybraincompare.report.qa module
qa.py: part of pybraincompare package
Functions to check quality of statistical maps
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pybraincompare.report.qa.
central_tendency
(data)[source]
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pybraincompare.report.qa.
count_voxels
(masked_in, masked_out)[source]
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pybraincompare.report.qa.
get_percent_nonzero
(masked_in)[source]
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pybraincompare.report.qa.
get_voxel_range
(nii_obj)[source]
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pybraincompare.report.qa.
is_only_positive
(nii_obj)[source]
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pybraincompare.report.qa.
is_thresholded
(nii_obj, brain_mask, threshold=0.95)[source]
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pybraincompare.report.qa.
outliers
(masked_data, n_std=6)[source]
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pybraincompare.report.qa.
t_to_z
(mr, dof)[source]
pybraincompare.report.webreport module
webreport.py: part of pybraincompare package
Functions to generate reports using qa tools
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pybraincompare.report.webreport.
run_qa
(mr_paths, html_dir, software='FSL', voxdim=[2, 2, 2], outlier_sds=6, investigator='brainman', nonzero_thresh=0.25, calculate_mean_image=True, view=True)[source]
Module contents