JISCMail - FSL Archives
FSL - FMRIB's Software Library . and assistancedogseurope.info using the mean >>>> across time >>>> 3. functional FLIRT (-in = is fslmaths'd output, -ref. I have an issue in using flirt command for FSL (). I used flirt and it flirt -in ROI. nii -ref assistancedogseurope.info -applyxfm -init assistancedogseurope.info -out assistancedogseurope.info But I get. FLIRT comes with a main GUI as well as three supporting guis: image which will be saved to the location specified in the Output image box.
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.
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.
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: The pre-requisites to use this method are: This script will either use an existing white-matter segmentation of the structural image, or create one itself, to define a white-matter boundary. We recommend that the structural image is bias-corrected separately beforehand if there is obvious bias field present. The script is also capable of using fieldmaps to perform simultaneous registration and EPI distortion-correction.
The inputs echospacing and pedir both refer to the EPI image not the fieldmap and are the same as required for FEATbut be careful to use the correct units. It can read and write ascii 4x4 matrices. In addition, it can be used to concatenate two transforms using -concat with the second transform or to find the inverse transformation using -inverse. If the option -mm is used then both input and output coordinates will be in mm coordinates, otherwise with -vox both coordinates will be in voxel coordinates.
For conversion between voxel and mm coordinates it is necessary to use either img2stdcoord or std2imgcoord see below. Note that the source coordinates can either be input via a file or via a pipe and for the latter the "-" symbol is used as the filename.
The format in either case is three numbers per line, space separated. To avoid this use the pipe input format or suppress the final line: The coordinates for the source image can be either in voxel coordinates default, or by explicitly using -vox or in mm coordinates using -mm.
This utility, and std2imgcoord are therefore useful for converting between voxel and mm coordinates within the same image, as well as for mapping coordinates between spaces. Converting from voxel to mm coordinates within the same image can be done with the command: It works the same way but transfers coordinates from "standard space" to the other image IMG space.
It can also convert between mm and voxel coordinates within the same image. 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.
flirt Command-line Program and Utilities
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.
flirt Command-line Program and Utilities
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: