NeuroRuler
Program that calculates head circumference from MRI data. 3D rotation, smoothing, and threshold options. Batch processes data via CLI. Imports and exports circumference and settings data.
Short demo
Links
Description
Cross-platform program that calculates head circumference from MRI data (.nii, .nii.gz, .nrrd). Supports 3D rotations and image smoothing and threshold options. Batch processes data via CLI. Imports and exports circumference and settings data in JSON format.
Installable via pip install NeuroRuler. Further instructions available on GitHub.
Made in COMP 523 (Software Engineering Lab) in collaboration with Madison Lester, Peifeng “Hank” He, and Eric Schneider for our client, Professor Martin Styner.
Figures
{
"input_image_path": "/Users/jesse/Documents/GitHub/COMP523/NeuroRuler/data/MicroBiome_1month_T1w.nii.gz",
"output_contoured_slice_path": "/Users/jesse/Documents/GitHub/COMP523/NeuroRuler/output/MicroBiome_1month_T1w/MicroBiome_1month_T1w_contoured.png",
"circumference": 285.04478394448125,
"x_rotation": -17,
"y_rotation": -18,
"z_rotation": 24,
"slice": 131,
"smoothing_conductance": 4.0,
"smoothing_iterations": 10,
"smoothing_time_step": 0.08,
"threshold_filter": "Otsu"
}
Example JSON input/output