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
4
3
#!/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
Thank you!
3
4
(3 Votes)
0
3
1
#!/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
Thank you!
1
3
(1 Votes)
0
4.29
7
#!/bin/sh
# Peaks: -x : output coordinates of the maximum intensity voxel
fslstats img -x
Thank you!
7
4.29
(7 Votes)
0
3.8
10
#!/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"}'
Thank you!
10
3.8
(10 Votes)
0
Are there any code examples left?
New code examples in category Shell/Bash
