FSL

# Flirt GUIs |

# AVAILABLE GUIs

FLIRT comes with a main GUI as well as three supporting guis:

- ApplyXFM - for applying saved transformations and changing FOVs
- InvertXFM - for inverting saved transformations
- ConcatXFM - for concatenating saved transformations

These support GUIs are self-explanatory and perform functions that are detailed in the command line versions.

Only the main FLIRT GUI is described in the rest of this page.

# MAIN FLIRT GUI

## MAIN OPTIONS

The simplest use of FLIRT is to register two single volumes together. This is done by choosing the Input image -> Reference image mode in the top box, then filling in the Reference image and Input image boxes with the appropriate images. The result is a registered image which will be saved to the location specified in the Output image box. All other options/boxes can be left at their default values.

The second mode of operation is a two stage registration which takes an input Low res image and two target images. It initially registers the low res image to a High res image and then registers this high res image to the final Reference image. The two resulting transformations are concatenated and then applied to the original low res image to create an Output image that is a version of the low res image transformed (resliced) to the reference image space.

#### Secondary Images

Apply the estimated transform to other (secondary) images, which were originally aligned with the input/low-res image, in order to align them with the reference image.

#### Model/DOF

Restrict the transformation type. For 3D to 3D mode the DOF can be set to 12 (affine), 9 (traditional), 7 (global rescale) or 6 (rigid body). In 2D to 2D mode only 3 DOF (rigid body) transformations are allowed.

## ADVANCED OPTIONS

The four categories of options are:

- Search - select the angular range over which the initial optimisation search stage is performed.
- Cost Functions - select the desired cost function from a range of inter- and intra-modal functions.
- Interpolation - select the interpolation method to be 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). The options for this final interpolation method are: Tri-Linear; Nearest Neighbour and Sinc. If Sinc is chosen, further window parameters (type of windowing function and window width) can also be specified.
- Weighting Volumes - impose voxel-wise weighting to reference and/or input images, to affects the cost function. The weighting images must be the same size as the image they are weighting (e.g. refweight and reference images) and the voxel values of the weighting image represent how much weighting that particular voxel is given in the cost function. 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. In this way very accurate registrations can be made between pathological and ``normal'' images. This cannot be achieved by masking the images prior to registration, as that induces artificial boundaries which bias the registration. Furthermore, some areas can be given extra weighting (such as the ventricles) so that the registration is most accurate near these structures, but still uses information from the rest of the image (e.g. the cortical surface) to improve the robustness of the registration.

#### Mark Jenkinson
FMRIB Image Analysis Group
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