segmentation_statistics¶
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nighres.statistics.
segmentation_statistics
(segmentation, intensity=None, template=None, statistics=None, output_csv=None, atlas=None, skip_first=True, ignore_zero=True, save_data=False, overwrite=False, output_dir=None, file_name=None)[source]¶ Segmentation Statistics
Compute various statistics of image segmentations
Parameters: - segmentation (niimg) – Input segmentation image
- intensity (niimg, optional) – Input intensity image for intensity-based statistics
- template (niimg, optional) – Input template segmentation for comparisons
- statistics ([str]) – Statistics to compute. Available options include: “Voxels”, “Volume”, “Center_of_mass”, “Mean_intensity”, “Std_intensity”, “10_intensity”,”25_intensity”,”50_intensity”, “75_intensity”,”90_intensity”, “Median_intensity”,”IQR_intensity”, “SNR_intensity”,”rSNR_intensity”, “Volumes”, “Dice_overlap”, “Jaccard_overlap”, “Volume_difference”, “False_positives” “False_negatives”, “Dilated_Dice_overlap”,”Dilated_false_positive”, “Dilated_false_negative”, “Dilated_false_negative_volume”, “Dilated_false_positive_volume”, “Center_distance”, “Detected_clusters”, “False_detections”, “Cluster_numbers”, “Mean_cluster_sizes”, “Cluster_maps”, “Average_surface_distance”, “Average_surface_difference”, “Average_squared_surface_distance”, “Hausdorff_distance”
- output_csv (str) – File name of the statistics file to generate or expand
- atlas (str, optional) – File name of an atlas file defining the segmentation labels
- skip_first (bool, optional) – Whether to skip the first segmentation label (usually representing the background, default is True)
- ignore_zero (bool, optional) – Whether to ignore zero intensity values in the intensity image (default is True)
- save_data (bool, optional) – Save output data to file (default is False)
- overwrite (bool, optional) – Overwrite existing results (default is False)
- output_dir (str, optional) – Path to desired output directory, will be created if it doesn’t exist
- file_name (str, optional) – Desired base name for output files with file extension (suffixes will be added)
Returns: Dictionary collecting outputs under the following keys (suffix of output files in brackets)
- csv (str): The csv statistics file
- map (niimg): Map of the estimated statistic, if relevant (stat-map)
Return type: Notes
Original Java module by Pierre-Louis Bazin.