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Fix mri brightness contrast #746

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merged 2 commits into from
Apr 18, 2024
Merged

Fix mri brightness contrast #746

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7929615
FIX: Set Nifti (MRI) window level and width based on 2-98 percentiles
vhosouza Apr 18, 2024
7d0208e
FIX: Typo in control.py code
vhosouza Apr 18, 2024
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19 changes: 17 additions & 2 deletions invesalius/control.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1039,8 +1039,23 @@ def OpenOtherFiles(self, group):
hdr = group.header
hdr.set_data_dtype('int16')

wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
ww = float((scalar_range[1] - scalar_range[0]))
# Calculate the 2% and 98% percentile
percentile_2 = np.percentile(self.matrix, 2)
percentile_98 = np.percentile(self.matrix, 98)

# define ww and wl based on 2-98 percentiles saturates
# the high pixel intensities that usually cause the image to
# and makes the brightness and contrast more similar across
# different types of scanners
# this solves the visualization issue only for MRIs imported with NIfTI, but not
# with DICOM
wl = float((percentile_2 + percentile_98) * 0.5)
ww = float((percentile_98 - percentile_2))

# Set wl and ww based on full scalar range. This causes some mri to be visualized
# very dark due to presence of high pixel intensities
# wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
# ww = float((scalar_range[1] - scalar_range[0]))

self.Slice = sl.Slice()
self.Slice.matrix = self.matrix
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