fslmaths
#!/bin/sh
# Any image containing NANs may not be read correctly
# by fslmaths or fslstats.
# -nan : replace NaNs (improper numbers) with 0
fslmaths img -nan img_no_nansfslmaths
#!/bin/sh
# Any image containing NANs may not be read correctly
# by fslmaths or fslstats.
# -nan : replace NaNs (improper numbers) with 0
fslmaths img -nan img_no_nansfslmaths
# FSL: fsl dilate or fsl erode:
# Kernel operations (set BEFORE filtering operation if desired):
# -kernel 3D : 3x3x3 box centered on target voxel (set as default kernel)
# -kernel 2D : 3x3x1 box centered on target voxel
# Spatial Filtering operations:
# N.B. all options apart from -s use the default kernel or that
# previously specified by -kernel
# -dilM : Mean Dilation of non-zero voxels
# -dilD : Modal Dilation of non-zero voxels
# -dilF : Maximum filtering of all voxels
# -dilall : Apply -dilM repeatedly until the entire FOV is covered
# -ero : Erode by zeroing non-zero voxels when zero voxels found in kernel
# -eroF : Minimum filtering of all voxels
# dilation example
# -odt sets the output data type.
# odt options are char short int float double
fslmaths mask -kernel 3D -dilM mask -odt short
# erosion example
fslmaths mask -kernel 2D -ero mask -odt shortfslmaths
#!/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_5pfslmaths
#!/bin/sh
# Add 100 to every voxel in image (making the image uniformly brighter)
fslmaths img -add 100 img_brightfslmaths
#!/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_inversefslmaths
#!/bin/sh
# Make an outline from a mask (using the -edge flag)
fslmaths mask -edge mask_outlinefslmaths
#!/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_difffslmaths
#!/bin/sh
# Make image containing positive values only by thresholding at 0
fslmaths img -thr 0 img_posfslmaths
#!/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 0fslmaths
#!/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_maskCopyright © 2021 Codeinu
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