FLIRT - FslWiki
This document gives a brief description of flirt and the various command-line programs available in the FLIRT component of FSL. More flexible DOF options are provided by the specific schedule files provided in $FSLDIR/etc/flirtsch. Currently just a light wrapper around FLIRT, with no modifications import pugliablog.info as fsl >>> from pugliablog.infog import example_data . a vtk mesh brain surface argument: ``-e`` padding: (a boolean) improve BET if FOV is very. FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated New in FSL5: the BBR method was implemented for improved EPI to.
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. 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 The default cost function is Correlation Ratio, which normally works well for all images. The main options are: In addition, FLIRT can also be used to apply a saved transformation to a volume -applyxfm, -init and -out.
flirt Command-line Program and Utilities
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. These guidelines should help in determining the correct value to use: For example, if the mask is being used to quantify values within an ROI and it is important to not include contamination from surrounding areas, then a high threshold should be used. Alternatively, if the mask is being used to define an exclusion ROI then it may be better to have a liberal border, which can be achieved with a low threshold.
Thresholding and binarising is done by fslmaths in the second call. Registrations with different numbers of DOF or different combinations of parameters can only be achieved using schedule files and the command line version of flirt.
Neuroimaging in Python - Pipelines and Interfaces — nipy pipeline and interfaces package
If the input images are 2D it is still necessary to use the -2D option as well. For more details see the section on available schedule files. Note that when the FOV is limited, but still 3D multiple slices then 2D or limited DOF transformations are normally required in order for the registration to be robust.FSL Tutorial 2: FEAT (Part 1)
In the registration stage it tries to find the transformation that best aligns the images, using a customised global optimisation technique that operates over multiple resolutions. Once the best transformation has been found the original input image is resampled, using the transformation found previously, to match the reference image.
FLIRT/UserGuide - FslWiki
That is, the final output image will contain intensities derived from the input image but will have a Field Of View FOV and voxel size that matches the reference image. If a higher or lower resolution version of the final image is required it is necessary to save the transformation from the registration stage and then apply it in a separate stage where a new reference is used to specify the desired voxel size and FOV.
Note that if a reference image is used it does not have to be the same image as in the registration and in fact the contents of the image the intensities are not used at all - only the voxel size and FOV are used.
At the command line, the transformation can be saved using the -omat option. This file can then be used for resampling by specifying it with the -init and -applyxfm options. That is, the resampling is done using flirt with the following syntax: To create a reference image of the appropriate size, if none already exists, use fslcreatehd to make a blank image one filled with zeros of appropriate dimensions.
Note that in previous versions fslcreatehd did not create an image, only the. Note that when changing the FOV rather than the voxel size, the bottom left corner remains fixed. In order to resample to a smaller FOV but keep say the Centre of Volume COV in the centre of both images it is necessary to add an extra translation to the transformation file.