FslMelodic

FslMelodic is a Java gui wrapper for the FSL 3.0 melodic program. MELODIC (Multivariate Exploratory Linear Optimized Decomposition into Independent Components) uses ICA (Independent Component Analysis) to decompose 4D data (for example FMRI data) into different interesting spatial and temporal components. It can pick out different activation and artefactual components without any model being specified. Thus the output is a new 4D data set (each volume being a separate spatial component) and a text file of separate time courses (temporal components).

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

Invocation

java  FslMelodic

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

java GlobalDesktop
java GlobalWorkbench
java FslToolChest

FslMelodic window

Information to be entered

Input
- Input
  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:
  - Image File: this allows one file to be selected as input.
  - Image Directory: this allows a directory to be selected as input. All analyze images (.img/.hdr) in the directory will be run through fast.
  - Image Filelist: this allows an ASCII file list to be selected as input; each filename listed in the list will be run through fast.
- Options
  Use this button to access input options.
  - Skull removal Options
    Pick one of the following:
    - None
      Do not extract the brain at all (--nobet)
    - Extract brain using BET
      default; this option uses bet to strip the skull off of the input image.
    - Specify threshold
      Allows user to specify the threshold to strip the skull from the image. (--bgthreshold)
Output
- Directory
  Specify the directory of the output file.
- Web Report
  Check this box to have melodic create a web report.
- Verbose Output
  Check for verbose output.
- Options
  Use this button to access output options.
  - Output File Types
    Pick one of the following:
    - whitening/dewhitening matrices
      Allows output of whitening/dewhitening matrices
    - PCA results
      Allows output of the PCA results.
    - mean volume
      Allows output of the mean volume.
    - thresholded and probability maps
      Allows output of the thresholded maps and probability maps.
    - original ICs
      Allows output of the original ICs.
    - unmixing matrix
      Allows output of the unmixing matrix.
Advanced...
This button toggles the Advanced Options panel that allows access to additional controls.
- Dimensionality Estimation Options
  Choose one of the following:
  - Automatic
    Allows for automatic dimensionality estimation.
  - Reduction into number of dimensions
    Specify the number of dimensions for dimensionality reduction.
  - Specify a technique
    Choose dimensionality estimation technique from lap, bic, mdl, aic and mean. lap is default.
- Independent Components Options
  - Number of ICs to extract
    Specify the number of IC's to extract.
  - Approach for ICA estimation
    Choose an approach for ICA estimation; choices are defl and symm.
  - Use mixture modelling on IC maps
  - Filename for mixture modelling of IC components
- Voxel-wise weights for the covariance matrix
  Specify the voxel-wise weight file for the covariance matrix. Must be in 3d+time format.
- Threshold for Mixture Model based inference
  Specify the threshold to use for mixture model based inferences.
- TR (sec)
  Specify the TR in seconds here.
- Use variance normalizations on timecourses
  Unchecking will switch off variance normalization.
- Calculate log power for frequency spectrum
  Allow calculation of log power for the frequency spectrum.
- Maximums and Minimums
  - Maximum number of iterations before restart
    Specify maximum number of iterations before restart.
  - Maximum number of restarts
    Specify maxiumum number of restarts.
  - Minimum error change
    Specify minimum error change.
- Masking Options
  Pick one of the following:
  - Automatic
    Allows for automatic masking.
  - Turn off
    Turn off masking completely.
  - Specify filename of mask for thresholding
    Choose a file that melodic will use for masking.

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