VARIABLES. There are two types of data variables that are manipulated in a schedule file: scalar and matrix data. Coordinates mapping, support SPM, ANTs and FSL linear and non-linear. % transformation. %. % Please use (can also use the inverse transformation in some cases like ANTs or FLIRT). % It can be: 4*4 affine matrix as mat file (vox to mm affine) . Check input coordinates, XYZ_vx should be column vector: 3*N or 4*N. This command allows to convert the transformation matrix provided by FSL's flirt command and ITK's linear transformation format to a format usable in MRtrix.
Using this weighting volume in either the GUI or command line registration calls should improve the fit in this region. This works in either registration mode where it is finding the transformation that aligns the input and reference images and also in applyxfm mode where it is applying a saved transformation to the input image.
Note that only in registration mode does it use the intensity information from the reference image. To apply saved transformations, the GUI ApplyXFM can also be used which provides the option of specifying the number of voxels and voxel size directly. There are two main types of cost function: If you are registering two images of different modality then you must use an inter-modal cost function, whereas for images of the same modality either can be used, although the intra-modal options may be more accurate.
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Within each category there is not much to choose from - it is a practical, experience-based decision. The recommended options to try first are: 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.
Note that for difficult registrations there is a translation only schedule file which is effectively 3 DOF, but only includes x,y,z translations. This is useful for obtaining initial position estimates when matching small FOV to large FOV, and can then be further refined. Transforming masks with FSL requires a little extra care.03 Transformation Matrices for Translation
To steps are needed: 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.
The threshold used with fslmaths should be set depending on the intended use of the output mask. 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.
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. 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. 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: A sequence of three scales A sequence of three translations A sequence of three rotations, in radians.
Or, if angles is False, a rotation matrix.
If the origin parameter is set to centre the defaultthis function assumes that voxel indices correspond to the voxel centre. For example, the voxel at 4, 5, 6 covers the space: In this case, a voxel at 4, 5, 6 covers the space: If the boundary parameter is set to high, the high voxel bounds are reduced by a small amount specified by the offset parameter before they are transformed to the world coordinate system.
If boundary is set to low, the low bounds are increased by a small amount.
transformconvert — MRtrix documentation
The boundary parameter can also be set to 'both', or None. This option is provided so that you can ensure that the resulting bounds will always be contained within the image space. A tuple containing the low, high bounds for each requested world coordinate system axis. If True, the points are treated as vectors - the translation component of the transformation is not applied.
If you set this flag, you pass in a 3, 3 transformation matrix. The points in p, transformed by xform, as a numpy array with the same data type as the input.