FLIRT/UserGuide - FslWiki
Aug 5, Most data in a schedule file is manipulated in matrix form. remaining 16 a reshaped version of the 4 by 4 affine matrix that corresponds to that cost axes, returning the result in U (NB: previous transform values are ignored). M = MAKEFSLXFMMATRIX(T,R,S,FILENAME) outputs a 4x4 transformation matrix This file is compatible with FSL's flirt and thus can be directly used without. In this case the FSL tool for linear registration, FLIRT, has been used to in the files misjon.info and misjon.info and store 4 by 4 matrices that.
Make FSL-compatible Transformation Matrix - File Exchange - MATLAB Central
For 2D images single slices you must use one of the valid 2D degrees of freedom options or -2D and appropriate schedules from the command line - see below If there is large bias field slow intensity variation - especially near the end slices then try using fast to create a restored image one with no bias field and then register using the restored image.
If there are relatively small errors in some crucial region of interest e. To do this a weighting image must be made which has the value of 1. 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.
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.
- Select a Web Site
- FLIRT schedule language reference
- Example Box: Spatial Transformations
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. 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.
However, if only ascii files are used no volumes need to be specified as in the example usage. Note that the source coordinates need to be stored in a file as three numbers per line, space separated.
flirt Command-line Program and Utilities
This requires the Talairach volume to have the origin coordinates and voxel dimensions entered in the correct analyse header fields. It works the same way but transfers coordinates from Talairach space to the other image IMG space. Note that it always uses trilinear interpolation, while 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. Using this lower resolution is sufficient for running registrations to obtain the spatial transformations. It is also possible to apply the spatial transformation to the original image to obtain a higher resolution result.
FSL:FLIRT - LCNIWiki
The following command will create an image with 1mm resolution, and using the whole image, not just the brain-extracted version: Also note that this output contains all the non-brain structures as well. If you wanted to have a high resolution version of the brain-extracted image instead then repeat the above command but replace S This image represents the nonlinear spatial transformation in the native format for FSL a coefficient filewhich is similar to a low resolution representation of a warp field.
This is a 4D volume, consisting of three 3D volumes: Each volume represents a component of the warp or displacement vectors: Load this image and place the cursor at the voxel location 27, 41, Look at the intensity values at this location in the different volumes, which should be: This represents the amount that this voxel has been moved by the transformation i.
It is this information that completely defines the transformation. Either of these files the warp or the coef can be used to apply this transformation to other images. Inspect the images and verify how much better the alignment is by comparison with the previous linear registrations.