FslFlirt

FslFlirt is a Java gui wrapper for the FSL 3.0 flirt program. FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

For more information about the FSL package, see the FSL(FMRIB Software Library) homepage.
FSL documentation on flirt.
Man page to the flirt application.

Invocation

java  FslFlirt

This starts up the java interpreter and runs the FslFlirt application. You need to have set up your environment for java in order for this to work. FslFlirt is also available in the FslToolChest, GlobalWorkbench and GlobalDesktop computing environments.

java GlobalDesktop
java GlobalWorkbench
java FslToolChest

FslFlirt window

Information to be entered

Input
- File
  Use the drop down menu to select an input type,and then use browse to select your input image files. Input types are as follows:
  - File: this allows one file to be selected as input.
  - Directory: this allows a directory to be selected as input. All analyze images (.img/.hdr) in the directory will be run through fast.
  - File List: this allows an ASCII file list to be selected as input; each filename listed in the list will be run through fast.
- Reference
  Choosing this option allows selection of a reference volume.
- ApplyXFM transformation
  Choosing this option applies transform with no optimization. It requires specifying an init file.
- Advanced Inputs...
  Click this button to access more input options.
  - Initial transform matrix
    Allows the input of the initial transform matrix. Flirt will autodetect the file's format, ascii or MEDx.
  - Weight Volumes
    - Reference
      Specify the volume to use for the reference weight.
    - Input
      Specify the volume to use for the input weight.
  - ApplyXFM Options
    - Force isotropic resampling (scale)
      applies transform with applyxfm but forces isotropic resampling using specified scale.
    - Interpolate outside image by size (voxels)
      Used for applyxfm, this option allows specification of voxels used in interpolation outside image by size.
Output
- Image Prefix
  Enter the output directory/prefix here that flirt will use to name its output files.
- Advanced Outputs...
  Click this button to access more output options.
  - Final transform matrix
    This option tells flirt to output a matrix in 4x4 ASCII format, using the filename specified.
  - MEDx format matrix
    This option tells flirt to output a matrix in MEDx format, using the filename specified.
  - Force datatype
    Choose a datatype here, and flirt will force the output datatype. Choices are character, short, int, float or double.
  - Final Interpolation Method
    Set the final interpolation method here. Choices are: Trilinear, Nearest Neighbour and Sinc. Default is Trilinear.
  - Sinc Options
    - Width (voxels)
      Specify the full sinc width, in voxels, here. Default number of voxels is 7.
    - Window
      Set the sinc window type here. Choices are: Hanning, Blackman and Rectangular. Rectangular is default.
Verbosity Level
Specify desired verbosity level here. 0 is least and default, 5 is most verbose.
Pause at each stage
Causes flirt to pause at each stage; default is off
Advanced Algorithm Options...
Click this button to access advanced options for flirt.
- Cost and Model Options
  - Cost Function
    Set the cost here. Choices are: Normalized Correlation, Correlation Ratio, Normalized Mutual Information, Mutual Information, and Least Squares. Default is Correlation Ratio
  - Rigid Body Model
    Specify the number of degrees of freedom that will be used in transformation. Allowable values are 2d rigid body mode, 12, 9, 7, and 6. In flirt, 12 is the default number of degrees of freedom.
  - Expert...
    Click this button to access expert options for flirt.
    - Angle Representation
      Set the angle representation here. Choices are: Quaternion and Euler; default is Euler.
    - Force Scaling
      Checking this box will force rescaling on all images, even the low-resolution images.
    - Number of Histogram Bins
      Specify the number of histogram bins in this box. Default number is 256.
- Search Strategy Options
  - Search Cost function
    Set the search cost here. Choices are: Normalized Correlation, Correlation Ratio, Normalized Mutual Information, Mutual Information, and Least Squares. Default is Correlation Ratio.
  - Search Resolution
    - Coarse (degrees)
      Specify the delta angle for a course search here. 60 degrees is default.
    - Fine (degrees)
      Specify the delta angle for a fine search here. 18 degrees is default.
  - Angles
    - No angular searching
      Allow or disallow angular searching. Sets all angular search ranges to 0 0.
    - X-axis(degrees)
      Set min and max X axis search ranges here. -90, 90 is default.
    - Y-axis(degrees)
      Set min and max Y axis search ranges here. -90, 90 is default.
    - Z-axis(degrees)
      Set min and max Z axis search ranges here. -90, 90 is default.
  - Sampling
    - Change input sampling
      This checkbox toggles the option to change input sampling.
    - Minimum voxel dimensions (mm)
      This sets the minimum voxel dimension for sampling. Units are in mm.

Last updated Thu Apr 10 13:22:12 EDT 2003