pybraincompare.report package

Submodules

pybraincompare.report.animate module

pybraincompare.report.animate.animate_figure()

pybraincompare.report.colors module

colors.py: part of pybraincompare package Color stuffs

pybraincompare.report.colors.get_colors(N, color_format='decimal')

pybraincompare.report.colors.peterson_roi_labels(colors=True)

pybraincompare.report.colors.random_colors(N)

pybraincompare.report.histogram module

histogram.py: part of pybraincompare package Functions for histograms

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)

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)

pybraincompare.report.histogram.plot_histogram(image, title='Image Histogram', height=400, width=1000, view_in_browser=True, bins=25, remove_zeros=True)

pybraincompare.report.image module

image.py: part of pybraincompare package Functions for static images

pybraincompare.report.image.make_anat_image(nifti_file, png_img_file=None)

pybraincompare.report.image.make_glassbrain_image(nifti_file, png_img_file=None)

pybraincompare.report.image.make_roi_image(nifti_file, png_img_file=None)

pybraincompare.report.image.make_stat_image(nifti_file, png_img_file=None)

pybraincompare.report.image.plot_vline(cur_val, label, ax)

pybraincompare.report.qa module

qa.py: part of pybraincompare package Functions to check quality of statistical maps

pybraincompare.report.qa.central_tendency(data)

pybraincompare.report.qa.count_voxels(masked_in, masked_out)

pybraincompare.report.qa.get_percent_nonzero(masked_in)

pybraincompare.report.qa.get_voxel_range(nii_obj)

pybraincompare.report.qa.header_metrics(image)

pybraincompare.report.qa.is_only_positive(nii_obj)

pybraincompare.report.qa.is_thresholded(nii_obj, brain_mask, threshold=0.95)

pybraincompare.report.qa.outliers(masked_data, n_std=6)

pybraincompare.report.qa.t_to_z(mr, dof)

pybraincompare.report.webreport module

webreport.py: part of pybraincompare package Functions to generate reports using qa tools

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)

Module contents