Fslmaths

#!/bin/sh

# Subtract one mask from another.  Binarize the resulting difference
# with -bin to get rid of negative numbers. See the jaccard index to expand on this use.

fslmaths mask1 -sub mask2 -bin mask_diff

Fslmaths

#!/bin/sh

# Make an empty image (same dimensions as input image). 
# See also fslhd.

fslmaths img -sub img empty_img # subtract the image from itself
# OR
fslmaths img -mul 0 empty_img  # mulitply the image by 0

Fslmaths

#!/bin/sh

# Make image containing positive values only by thresholding at 0

fslmaths img -thr 0 img_pos

Fslmaths

#!/bin/sh

# Multiply image by mask to extract just those voxels 
# from image that are in the mask (see also -mas):

fslmaths img -mul mask img_in_mask

Fslmaths

#!/bin/sh

# Apply multiple ordered operations: 
# multiplication followed by thresholding 
# and then making the image binary

fslmaths img -mul gm_mask -thr 0.5 -bin img_gm_bin

Fslmaths

#!/bin/sh

# Mask one image with another using -mas (similar to multiplying 
# with -mul, but more robust): 
# if the mask is a label image, that should be okay.

fslmaths img -mas mask -bin img_bin

Fslmaths

#!/bin/sh

# Make a 5 percent mask (default choice for fdt results).
# fdt is FSL's diffusion toolbox.
# Use following percentage (0-100) of ROBUST RANGE of 
# non-zero voxels and threshold below that percentage

fslmaths img -thrp img_5p

Fslmaths

#!/bin/sh

# Add 100 to every voxel in image (making the image uniformly brighter)

fslmaths img -add 100 img_bright

Fslmaths

#!/bin/sh

# Make an outline from a mask (using the -edge flag)

fslmaths mask -edge mask_outline

Fslmaths

#!/bin/sh

# Make an inverse binary image mask (switch the 1s and 0’s)

# Create the inverse mask (Mark Jenkinson's approach. Very clever:
# Multiply by negative 1, then add 1). Make sure you pass in a binary mask)

fslmaths mask -mul -1 -add 1 -bin mask_inverse 

# OR use -binv flag

fslmaths mask -binv mask_inverse

Similar codes

1 vote205 views1 answer
Bash perform operation on all files in directory
Shell/Bash
3 votes219 views3 answers
Git branch change remote
Shell/Bash
1 vote202 views1 answer
Mysql specify a socket
Shell/Bash
0 vote217 views1 answer
Install onenote in ubuntu
Shell/Bash
0 vote225 views1 answer
Git remove tag from remote
Shell/Bash
1 vote209 views1 answer
Ubuntu add public key to server
Shell/Bash
0 vote197 views1 answer
Trash folder linux
Shell/Bash
0 vote221 views1 answer
Restart ubuntu 18.04 server
Shell/Bash
13 votes264 views1 answer
Sourcetree change commit message
Shell/Bash
9 votes227 views2 answers
How to ssh to another computer
Shell/Bash