fsl stats
#!/bin/sh
if [ $# -lt 1 ] ; then
echo "Usage: $0 <filename>" ;
exit 1 ;
fi
img=$(remove_ext ${1})
min=$(fslstats ${img} -R | awk '{ print $1 }')
max=$(fslstats ${img} -R | awk '{ print $2 }')
scaling=$(echo "scale=5; 255.0 / ( $max - $min )" | bc)
fslmaths ${img} -sub ${min} -mul ${scaling} ${img}_scaled
# If you want all the values to be integers, then change
# the odt (output datatype):
fslmaths ${img}_scaled ${img}_int_scaled -odt intfsl stats
#!/bin/sh
# Get mean (-M) and standard deviation (-S) of a masked (-k) region
# (e.g., a statistical image)
fslstats img_stats -k mask -M -S
# Test if an image is a binary mask:
# -M gets the mean of non-zero voxels.
# -S gets the standard deviation of non-zero voxels.
# Beware of images containing NANs!
# The mean should be 1
# The standard deviation should be 0
fslstats img_mask -M -Sfsl stats
#!/bin/sh
# List co-ordinates of each labeled region in an atlas with fslstats.
# Use preoption -K < indexMask > will generate seperate n submasks from
# indexMask, for indexvalues 1..n where n is the maximum index value
# in indexMask, and generate statistics for each submask.
fslstats -K myLabelAtlas myLabelAtlas -xCopyright © 2021 Codeinu
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