fslstats code example

Example 1: fslstats

#!/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 -x

Example 2: fslstats

#!/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 -S

Example 3: fslstats

#!/bin/sh

# Get the voxel count for a mask
fslstats mask -V | awk '{printf $1 "\n"}'

# Get the volume in cubic mm for a mask
fslstats mask -V | awk '{printf $2 "\n"}'

Example 4: fslstats

#!/bin/sh

# Peaks: -x : output coordinates of the maximum intensity voxel 

fslstats img -x

Example 5: fslstats

#!/bin/sh

# Center of gravity: 
# -C : output centre-of-gravity (cog) in voxel coordinates 
# -c : output centre-of-gravity (cog) in mm coordinates 

fslstats mask -C -c