flirt Command-line Program and Utilities
from tankekraft.infoaces import fsl >>> from tankekraft.infog import example_data >> > aw = fsl. Currently just a light wrapper around FLIRT, with no modifications. Use flirt. For example to register a functional to a structural: $ flirt -ref highres FAST gives out a 3D bias image so multiply a 4D input by bias field using . echo "check result of skull stripping in fslview and close when done". """The fsl module provides classes for interfacing with the `FSL . argstr='-F', xor= _xor_inputs, desc="apply to 4D fMRI data") 'flirt -in tankekraft.info -ref tankekraft.info - out tankekraft.info -omat result = tankekraft.info() # doctest: +SKIP. """.
See also the list of common example usages. The main options are: In addition, FLIRT can also be used to apply a saved transformation to a volume -applyxfm, -init and -out.
For this usage the reference volume must still be specified as this sets the voxel and image dimensions of the resulting volume. Cost Function Weighting Weighting volumes can be specified using -refweight, -inweight or both. Note that this is different from masking the original images, as masking introduces artificial boundaries whereas weighting does not. Note that it does not perform any search in 2D mode, and cannot deal with 2D to 3D registrations.
Interpolation Methods This includes Nearest Neighbour and a family of Sinc-based methods three window types - rectangular, Hanning and Blackman with configurable window width. The interpolation is only used for the final transformation and in applyxfmnot in the registration calculations. It can read and write ascii 4x4 matrices and MEDx transforms. In addition, it can be used to concatenate two transforms using -concat with the second transform or to find the inverse transformation using -inverse.
As MEDx transformations require voxel dimensions, the input and reference volume corresponding to the transformation must be specified when using this command. Note that this is different from masking the original images, as masking introduces artificial boundaries whereas weighting does not.
Note that it does not perform any search in 2D mode, and cannot deal with 2D to 3D registrations. Interpolation Methods This includes Nearest Neighbour, a family of Sinc-based methods three window types - rectangular, Hanning and Blackman with configurable window width, and spline a highly efficient method, with similar output characteristics to sinc.
FSL:Registration - LCNIWiki
The interpolation is only used for the final transformation and in applyxfmnot in the registration calculations. In addition, there is the BBR cost function which utilises a segmentation of the reference image to define a boundary, and it is the intensity differences in the input image, across the transformed boundary, that contribute to the cost.
The pre-requisites to use this method are: This script will either use an existing white-matter segmentation of the structural image, or create one itself, to define a white-matter boundary. We recommend that the structural image is bias-corrected separately beforehand if there is obvious bias field present.
The script is also capable of using fieldmaps to perform simultaneous registration and EPI distortion-correction.
Neuroimaging in Python - Pipelines and Interfaces — nipy pipeline and interfaces package
The inputs echospacing and pedir both refer to the EPI image not the fieldmap and are the same as required for FEATbut be careful to use the correct units.
It can read and write ascii 4x4 matrices. In addition, it can be used to concatenate two transforms using -concat with the second transform or to find the inverse transformation using -inverse.
If the option -mm is used then both input and output coordinates will be in mm coordinates, otherwise with -vox both coordinates will be in voxel coordinates. For conversion between voxel and mm coordinates it is necessary to use either img2stdcoord or std2imgcoord see below. Note that the source coordinates can either be input via a file or via a pipe and for the latter the "-" symbol is used as the filename. The format in either case is three numbers per line, space separated.
To avoid this use the pipe input format or suppress the final line: The coordinates for the source image can be either in voxel coordinates default, or by explicitly using -vox or in mm coordinates using -mm. This utility, and std2imgcoord are therefore useful for converting between voxel and mm coordinates within the same image, as well as for mapping coordinates between spaces. Converting from voxel to mm coordinates within the same image can be done with the command: It works the same way but transfers coordinates from "standard space" to the other image IMG space.
It can also convert between mm and voxel coordinates within the same image. See the entry on img2stdcoord above.
Sinc interpolation is used internally. Appropriate options -applyxfm and -init to FLIRT can be used to apply transformations to single volumes with other interpolation methods.
A reference volume is required in order to determine the matrix size and FOV for the final volume. That is, it compares two transformations normally two possible registrations of the same volume pair to see how much they differ.
This is useful to compare alternative registrations. It calculates the average using an analytic formula applied over an 80mm sphere with the origin at the centre of gravity of the image for which it requires the input image to be specified. An alternative usage is to provide a mask as the fourth argument which is then used to specify the ROI, rather than using the sphere.
In this mode it gives two outputs: With this calculation it does not require an origin to be set.
flirt Command-line Program and Utilities
In order to set the centre of rotation it requires the input volume also called the reslice volume. Naturally, any filenames you wish to use can be chosen.
Note that -dof was used as the default would otherwise be