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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.

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. 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.

Step-by-Step Guide

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.

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. 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.

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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.

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 command line calls made in a two-stage registration of imageA to imageB to imageC are as follows: Note that the first two calls to flirt would normally require the cost function or degrees of freedom dof to be set in the desired options.

In the final call to flirt the option -interp is useful for specifying the interpolation method to be used the default is trilinear. Also note that the FLIRT GUI outputs the command line calls used to effect the two stage registration, and will be similar to the above, although they will include specification of many of the default settings.

It is only possible to perform 2D registration on the command line using schedule files via the -schedule option. A list of currently provided schedule files is: How do I get the value of the cost function? You can measure the cost function between two images using: The cost value is the first number of the first line that is printed.

If you want to automatically select only this then you can do: A study-specific template is an average image created from a set of structural images which represent the particular study group.

However, for many applications this image will not represent the study group very accurately, say due to differing age or disease. Therefore it is desirable in these cases to create a study-specific template image. An affine template image as is the avgT1 can be created using the following steps: Choose a reference image from among the set Register each image in the set to the reference image, using flirt, and saving the output images e.

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.

More sophisticated schemes for making the target image less sensitive to the choice of the reference image can also be carried out.