FLIRT/UserGuide - FslWiki FLIRT/UserGuide - FslWiki

Fsl flirt, flirt flirt oh it hurts - Nullege Python Samples

Medical Image Analysis, 5 2, If the scanner voxel size may have changed due to calibration shifts then it is appropriate to use 7 DOF instead of 6 or 4 instead of 3 to compensate for global scale changes.

If Sinc is chosen, further window parameters type of fsl flirt function and window width can also be specified.

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The threshold used with fslmaths should be set depending on the intended use of the output mask. Read data from stdout and stderr, until end-of-file is reached.

FLIRT/Contents - FslWiki

Masks can be transformed from one space to another by using either one of the command line tools flirt or applywarp, or the ApplyXFM GUI. Accurate and robust brain image alignment using boundary-based registration. An additional step is inserted prior to step 1.

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With this calculation it does not require an origin to be set. A more efficient algorithms is then applied that exploits the separability of the problem. This process can be iterated several times if desired.

FMRIB Software Library v0

This script will either use an existing white-matter segmentation of the structural image, or create one itself, to define a white-matter boundary. If you want to automatically select only this then you can do: This should leave you with correctly named transform files which FEAT will automatically use when carrying out group statistics.

To apply a saved transformation to another image use: 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 fsl flirt a low threshold. You can measure the cost function between two images using: Sinc interpolation is used internally.

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. It works the same way but transfers coordinates from standard space to the other image IMG space.

Interpolation - select the interpolation method to fsl flirt used in the final reslice transformation it is not used for the estimation stage - trilinear interpolation is always used for the estimation of the transformation.


Using this weighting volume in either the GUI or command line registration calls should improve the fit in this region. A diagonal matrix can be specified by supplying a one-dimensional array-like to the matrix parameter, in which case a more efficient algorithm is applied.

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To avoid this use the pipe input format or suppress the final line: Register two images flirt -in invol -ref refvol -out outvol -omat invol2refvol. This can be done by adding the appropriate offsets in mm to the values in the right hand column first row is x, second is y, third is z of the transformation.

How do I do a two-stage registration using the command line? The weighting images must be the same size as the image they are weighting e. 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.

For each of the programs described here, a usage message which describes the full list of available options can be obtained by running the program with no options.

Step-by-Step Guide

This is useful for obtaining initial position estimates when matching small FOV to large FOV, and can then be further refined. Cost Function Weighting Weighting volumes can be specified using -refweight, -inweight or both.

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Note that it is advisable to check each registration manually, "by eye", in order to make sure that the average template image is not corrupted with a poor registration result. Therefore, by setting weights to zero, some areas of the image can be effectively ignored, which is useful in masking out pathologies so that they do not affect the registration.

The coordinates for the source image can be either in voxel coordinates default, or by explicitly using -vox or in mm coordinates using -mm.

The simplest of these is to redo the registration and averaging using the initial average image, from above, as the reference. At the command line, the transformation can be saved using the -omat option.

It can read and write ascii 4x4 matrices. Once the best transformation has been found the original input image is resampled, using the transformation found previously, to match the reference image.

There are two main types of cost function: Note that it does not perform any search in 2D mode, and cannot deal with 2D to 3D registrations.

A reference volume is required in order to determine the matrix size and FOV for the final volume.

See the entry on img2stdcoord above. Use the Group facility GUI only or scripting for running the registration on a collection of images.

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Cost Functions - select the desired cost function from a range of inter- and intra-modal functions. The order has to be in the range The interpolation is only used for the final transformation and in applyxfmnot in the registration calculations. Note that the source coordinates need to be stored in a file as three numbers per line, space separated.

Main Options

The format in either case is three numbers per line, space separated. Transforming masks with FSL requires a little extra care. Note that for difficult registrations there is a translation only schedule file which is effectively 3 DOF, but only includes x,y,z translations.

In order to set the centre of rotation it requires the input volume also called the reslice volume. This page describes our recommendations in such cases.

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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.

Check each step of the registration pathway separately as well as the total output, using FSLView to overlay the functional image resampled into structural space, and the structural image resampled into standard space Example result: Converting from voxel to mm coordinates within the same image can be done with the command: Also note that the.

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.