FslMcflirt

FslMcflirt is a Java gui wrapper for the FSL 3.0 mcflirt program. MCFLIRT is an intra-modal motion correction tool designed for use on fMRI time series and based on optimization and registration techniques used in FLIRT, a fully automated robust and accurate tool for linear (affine) inter- and inter-modal brain image registration.

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

Invocation

java  FslMcflirt

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

java GlobalDesktop
java GlobalWorkbench
java FslToolChest

FslMcflirt 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.
Output
- Image
  Use this option to specify the basename of the output file.
- Report progress to screen
  Check this box to see mcflirt's progress in the run window. Unchecking this will disallow choosing of a verbosity level.
- Verbosity Level
  This dropdown box allows selection of the level of verbosity that is desired from the output; 5 is the highest, 0 is the lowest and the default.
Advanced...
This button toggles the Advanced Options panel that allows access to additional controls.
- Inputs
  - Initial transform matrix
    Use this text box to specifiy the initial transform matrix that will be applied to all volumes. It is an optional parameter (-init).
- Outputs
  - Produce variance and std.dev. images
    Check this box, and mcflirt will produce variance and standard deviation images in the specified output directory.
  - Save transformation matrices
    Check this box, and mcflirt will save transformation matrices in a subdirectory called 'outfilename.mat'.
  - Save transformation parameters
    Check this, and mcflirt will save all transformation parameters in a file called 'outputfilename.par'.
  - Final output image interpolation
    Choose either tri-linear (default) or sinc kernel, which will apply the final transformations using the sinc kernel.
- Search Strategy Options
  - Number of stages
    Specify the number of search levels for mcflirt to use. Default is 3, but specify 4 if you want to use final sinc interpolation.
  - Compute cost function on gradient images
    Check this box to run a search on gradient images.
  - Compute cost on contour images
    Check this box to run a search on contour images.
- Reference Volume Options
  - Default [(number of volumes)/2]
    Specify this if you do not want to adjust any reference volume settings.dfhdf
  - Specify number of reference volumes
    This option registers to (n+1)th volume in series. Default is no_vols/2.
  - Register timeseries to mean volume
    This option register the timeseries to mean volume and overrides the refvol option.
- Cost and Model Options
  - Cost Function
    Choose the cost function you would like to use in mcflirt. Pick from Normalized Correlation Ratio, Mutual Information, Woods, Correlation Ratio, Normalized Mutual Information or Least Squares. The default is Normalized Correlation Ratio.
  - Model Degrees of Freedom
    Specify the number of transform dofs to be used by mcflirt. Default is 6.
  - Expert
    Click this button to view expert options.
    - Number of histogram bins
      Specify the number of histogram bins to be used by mcflirt. Default is 256.
    - Scaling factor
      Specify a scaling factor for mcflirt to use. Default is 6.0
    - Rotation optimization tolerance scaling factor
      Specify a scaling factor to be used for rotation optimization tolerances in mcflirt.
    - Cost Function Smoothing
      Use this parameter to control smoothing in the cost function. Default is 1.0.
  - Padding Options
    - Force padding of volume
      Check this box to force mcflirt to pad the volume.
    - Field of view (cm)
      Specify the size of the field of view to be used when padding a 2D volume. Default is 2cm.

Last updated Thu Apr 10 13:18:50 EDT 2003