Make FSL-compatible Transformation Matrix - File Exchange - MATLAB Central
Cheers. On 14 Apr , at , Matt Glasser wrote: > Hi, > > I am curious as to the exact format of the FLIRT transformation > matrix. I know that the fourth row. Linear transformation is only global scaling and rotation, — no translation a matrix multiplication. of the SPM2 and FSL package in spm normalise and flirt, respectively, see Table 7. 2 . guiadeayuntamientos.info string FILENAME. This file is compatible with FSL's flirt and thus can avscale reads a transformation matrix file and lists the corresponding translation, rotation .
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. The boundary parameter can also be set to 'both', or None. Appropriate options -applyxfm and -init to FLIRT can be used to apply transformations to single volumes with other interpolation methods.
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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.
FLIRT/UserGuide - FslWiki
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. Also note that the.
The transformation files are simply stored as ascii matrices, and so other conventions can be used which might be better for MATLAB users to avoid confusion although the. To apply a saved transformation to another image use: To perform a 3 DOF 2D single slice registration: Note that several other schedule files could be used - including 3D translation only schedules etc.
This page describes our recommendations in such cases. Take your FMRI data, with only a few slices. Now optionally take a high-resolution structural image, e. T1-weighted let's call this highres. Finally, identify your standard space image let's call this standard. Now you are ready to register these all together.
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.