FLIRT/UserGuide - FslWiki
There is also a button for this on the ApplyXFM menu. You can use applywarp instead of flirt if you prefer (it is a little easier and does not need the. Currently just a light wrapper around FLIRT, with no modifications nipype. cypenv.info as fsl >>> from cypenv.infog import example_data >>> applyxfm = fsl. I used flirt and it works well to co-register an image, say INPUT using flirt -in cypenv.info -ref cypenv.info -applyxfm -init cypenv.info -out cypenv.info But I get.
flirt Command-line Program and Utilities
The main options are: In addition, FLIRT can also be used to apply a saved transformation to a volume -applyxfm, -init and -out. For this usage the reference volume must still be specified as this sets the voxel and image dimensions of the resulting volume. Cost Function Weighting Weighting volumes can be specified using -refweight, -inweight or both. Note that this is different from masking the original images, as masking introduces artificial boundaries whereas weighting does not.
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 and a family of Sinc-based methods three window types - rectangular, Hanning and Blackman with configurable window width. The interpolation is only used for the final transformation and in applyxfmnot in the registration calculations.
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. 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.
Neuroimaging in Python - Pipelines and Interfaces — nipy pipeline and interfaces package
T1-weighted let's call this highres. 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: 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.
FLIRT/FAQ - FslWiki
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: