fsl.wrappers.fslmaths

This module provides the fslmaths class, which acts as a wrapper for the fslmaths command-line tool.

class fsl.wrappers.fslmaths.fslmaths(input)

Bases: object

Perform mathematical manipulation of images.

abs()

Absolute value.

bin()

Use (current image>0) to binarise.

binv()

Binarise and invert (binarisation and logical inversion).

recip()

Reciprocal (1/current image).

Tmean()

Mean across time.

Tstd()

Standard deviation across time.

Tmin()

Min across time.

Tmax()

Max across time.

fillh()

fill holes in a binary mask (holes are internal - i.e. do not touch the edge of the FOV).

ero(repeat=1)

Erode by zeroing non-zero voxels when zero voxels in kernel.

dilM(repeat=1)

Mean Dilation of non-zero voxels.

dilF(repeat=1)

Maximum filtering of all voxels.

add(image)

Add input to current image.

sub(image)

Subtract image from current image.

mul(image)

Multiply current image by image.

div(image)

Divide current image by image.

mas(image)

Use image (>0) to mask current image.

rem(image)

Divide current image by following image and take remainder.

thr(image)

use image number to threshold current image (zero < image).

uthr(image)

use image number to upper-threshold current image (zero anything above the number).

inm(image)

Intensity normalisation (per 3D volume mean)

bptf(hp_sigma, lp_sigma)

Bandpass temporal filtering; nonlinear highpass and Gaussian linear lowpass (with sigmas in volumes, not seconds); set either sigma<0 to skip that filter.

run(output=None)

Save output of operations to image.