MOESM1 of Semiautomatic segmentation of the kidney in magnetic resonance images using unimodal thresholding

Additional file 1. unimodcode.zip: a zipped folder containing the following files: unimodscript.py: the central script for the unimodal thresholding approach, l03threshSTD.py: the monomodal thresholding algorithm function, l02shrink.py: a function to remove most of the whitespace from a masked volume, detect_peaks.py: the peak detection function by Marcos Duarte, also available at https://github.com/demotu/BMC/blob/master/functions/detect_peaks.py , example.nii.gz: an anonymized abdominal MRI in NIfTI format, example_left_kidney_preseg.nii.gz: a manual pre-segmentation of the left kidney of the example MRI, done with the Multi-image Analysis GUI (MANGO), available at http://ric.uthscsa.edu/mango/ , example_right_kidney_preseg.nii.gz: a manual pre-segmentation of the right kidney of the example MRI, done with the Multi-image Analysis GUI (MANGO), available at http://ric.uthscsa.edu/mango/ , LICENSE.txt: the MIT license text, readme.txt: description of the included files, list of dependencies, instructions for installation and use

Correlation between the change of the Na⁺ concentration and the change of the area of the lower leg of acute heart failure patients during diuretic treatment.

<p>Correlation between the change of the Na⁺ concentration and the change of the area of the lower leg of acute heart failure patients during diuretic treatment.</p

Demographic data and results.

<p>Demographic data, [Na⁺] and H₂O content in the muscle, the skin and the lower leg, Na⁺/NT-proBNP blood levels and body weight in patients with acute heart failure before and after diuretic (furosemide) therapy and on the control group are presented (mean ± SD). <i>P</i>-values (two-tailed student’s t-test) and confidence intervals (95% confidence level) are shown. BT = before therapy, AT = after therapy, C = controls (healthy subjects). AU = arbitrary unit. NA = not applicable.</p><p>Demographic data and results.</p

Interreader reliability.

<p>The interreader reliability was evaluated for ²³Na measurements of 2 randomly selected probands which were assessed by four readers independently. Whole lower leg = grey-values > 2 x background noise. Skin = region where leg is positioned on the cylindrical phantom holders surface (one pixel-thickness = 3 mm). SD = standard deviation.</p><p>Interreader reliability.</p

Exemplary ²³Na/¹H-MRI-images of a patient with acute heart failure before and after diuretic treatment and of a matched healthy subject.

<p><b>Upper row:</b>²³Na scans (gradient echo ²³Na sequence) of a 71-year-old patient before and after heart failure therapy. The amount of Na⁺ in skin and subcutaneous tissues, as well as in skeletal muscle was reduced, compared to the 10, 20, 30, and 40 mmol/L NaCl solutions (below). At far right is a normal 71-year-old control person with little sodium in skin and muscle. <b>Lower row:</b> The same patient before and after furosemide and the control subject viewed with conventional (¹H) MRI (fat-suppressed inversion recovery (IR) sequence). The salt solutions appear white because of their water content.</p

Evaluation of the compartments of the lower leg.

<p>The compartments of the lower leg were determined before (left) and after (right) diuretic therapy by an experienced reader. The different anatomical regions of interest (ROI) were drawn guided by the anatomical image (lower images, T1-weighted fast-low-angle-shot (FLASH)-sequence). To measure the cutis one pixel was marked along the coil surface. The value of the whole lower leg = grey-values > 2 x background noise. Four tubes containing aqueous solutions with increasing Na⁺ concentrations (10, 20, 30, and 40 mmol/L NaCl) were positioned in a custom-made device positioned inside the coil just below the patient’s lower leg. Gray-scale measurements of the tubes served as calibration standards for ²³Na-MRI of the skeletal muscle and skin by relating intensity to a concentration in a linear trend analysis. For H₂O quantification, the 10 mmol/L NaCl tube served as a calibration standard for tissue water in a linear trend analysis defining a water content of approximately 1 liter water per liter volume. ROIs: 1 = cutis, 2 = triceps surae muscle, 3 = whole lower leg, 4–7 = calibration solutions, 8 = background noise.</p

Scanning protocol.

<p>Scanning protocol.</p