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.

fslmaths is unlike the other FSL wrapper tools in that it provides an object-oriented method-chaining interface, which is hopefully easier to use than constructing a fslmaths command-line call. For example, the following call to the fslmaths wrapper function:

fslmaths('input.nii').thr(0.25).mul(-1).run('output.nii')

will be translated into the following command-line call:

fslmaths input.nii -thr 0.25 -mul -1 output.nii

The fslmaths wrapper function can also be used with in-memory images. If no output file name is passed to the run() method, the result is loaded into memory and returned as a nibabel image. For example:

import nibabel as nib
input  = nib.load('input.nii')
output = fslmaths(input).thr(0.25).mul(-1).run()

__init__(input)

Constructor.

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. Set output to a filename to have the result saved to file, or omit output entirely to have the result returned as a nibabel image.

__run(*cmd)

Run the given fslmaths command.

__dict__ = mappingproxy({'__module__': 'fsl.wrappers.fslmaths', '__doc__': "Perform mathematical manipulation of images.\n\n ``fslmaths`` is unlike the other FSL wrapper tools in that it provides an\n object-oriented method-chaining interface, which is hopefully easier to\n use than constructing a ``fslmaths`` command-line call. For example, the\n following call to the ``fslmaths`` wrapper function::\n\n fslmaths('input.nii').thr(0.25).mul(-1).run('output.nii')\n\n will be translated into the following command-line call::\n\n fslmaths input.nii -thr 0.25 -mul -1 output.nii\n\n The ``fslmaths`` wrapper function can also be used with in-memory\n images. If no output file name is passed to the :meth:`run` method, the\n result is loaded into memory and returned as a ``nibabel`` image. For\n example::\n\n import nibabel as nib\n input = nib.load('input.nii')\n output = fslmaths(input).thr(0.25).mul(-1).run()\n ", '__init__': <function fslmaths.__init__>, 'abs': <function fslmaths.abs>, 'bin': <function fslmaths.bin>, 'binv': <function fslmaths.binv>, 'recip': <function fslmaths.recip>, 'Tmean': <function fslmaths.Tmean>, 'Tstd': <function fslmaths.Tstd>, 'Tmin': <function fslmaths.Tmin>, 'Tmax': <function fslmaths.Tmax>, 'fillh': <function fslmaths.fillh>, 'ero': <function fslmaths.ero>, 'dilM': <function fslmaths.dilM>, 'dilF': <function fslmaths.dilF>, 'add': <function fslmaths.add>, 'sub': <function fslmaths.sub>, 'mul': <function fslmaths.mul>, 'div': <function fslmaths.div>, 'mas': <function fslmaths.mas>, 'rem': <function fslmaths.rem>, 'thr': <function fslmaths.thr>, 'uthr': <function fslmaths.uthr>, 'inm': <function fslmaths.inm>, 'bptf': <function fslmaths.bptf>, 'run': <function fslmaths.run>, '_fslmaths__run': <function fslmaths.__run>, '__dict__': <attribute '__dict__' of 'fslmaths' objects>, '__weakref__': <attribute '__weakref__' of 'fslmaths' objects>})

__module__ = 'fsl.wrappers.fslmaths'

__weakref__

list of weak references to the object (if defined)