Neuroimaging in Python - Pipelines and Interfaces — nipy pipeline and interfaces package
This document gives a brief description of flirt and the various command-line programs available in the FLIRT component of FSL. applyxfm4D is a utility that transforms a 4D time series by applying known affine transformations to them. What determines the FOV and voxel size in FLIRT? than you wanted then the result can be easily inverted using InvertXFM or convert_xfm. Currently just a light wrapper around FLIRT, with no modifications import az-links.info as fsl >>> from az-links.infog import example_data >>> applyxfm = az-links.infocess. . to 4D fMRI data argument: ``-F`` mutually_exclusive : functional, reduce_bias, >>> az-links.info = >>> result = sus. run().
Here is a general checklist of things to test and try in order to improve the registration results please do not post a query to the FSL email list about registration results until you have gone through this list: 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. 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: 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.
JISCMail - FSL Archives
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.
flirt Command-line Program and Utilities
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. 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. It can read and write ascii 4x4 matrices and MEDx transforms. In addition, it can be used to concatenate two transforms using -concat with the second transform or to find the inverse transformation using -inverse. As MEDx transformations require voxel dimensions, the input and reference volume corresponding to the transformation must be specified when using this command.
However, if only ascii files are used no volumes need to be specified as in the example usage.