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Similar binary masks were created for cytoplasmic and nuclear compartments based on DAPI staining of nuclei.
Suitable thresholds were adjusted and kept constant for each slide, and binary masks were created.
Similar binary masks were created for cytoplasmic and nuclear compartments on the basis of DAPI staining of nuclei.
A total of 14 binary masks were created, covering major white matter pathways including right and left inferior longitudinal fasciculus (ILF), superior longitudinal fasciculus (SLF), uncinate fasciculus, anterior thalamic radiation (ATR), cingulum bundle, corticospinal tract (CST), corpus callosum, and fornix.
Manual approximate binary masks were created separately for the heart valves, papillary muscles, and larger trabecular structures (in places where they were sufficiently clearly separated from the endocardial surface) and superimposed on the segmented image stack to numerically tag each separate region with an identifier different to the normal myocardium.
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A cutoff for χr2 is selected by comparing all images; binary masks are created and saved.
A binary mask was created from the selected areas, and applied on the initial stack.
First, a binary mask is created, distinguishing foreground (plant) from the background.
A separate binary mask was created that identified the total tissue area in each image, so the final parameter of analysis was the area fraction.
To exclude surface points for which no meaningful thickness measure existed in a given subject, a binary mask was created based on the logical combination of regions in each subject where the thickness estimate was zero.
For each subject, a binary mask was created from the volume of TT voxels such that any voxel that met the significance criterion from the permutation test and belonged to a cluster of 40 or more voxels in size was assigned a value of 1.
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