FSL - MELODIC

Source: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC/FAQ#How_do_I_transform_the_MELODIC_results_from_a_low-resolution_space_to_a_higher-resolution_one.3F

 

 

Research Overview

MELODIC ( Multivariate Exploratory Linear Optimized Decomposition into Independent Components ) 3.0 uses Independent Component Analysis to decompose a single or multiple 4D data sets into different spatial and temporal components. For ICA group analysis, MELODIC uses either Tensorial Independent Component Analysis (TICA, where data is decomposed into spatial maps, time courses and subject/session modes) or a simpler temporal concatenation approach. MELODIC can pick out different activation and artefactual components without any explicit time series model being specified.

 

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Melodic GUI

To call the MELODIC GUI, either type Melodic in a terminal (type Melodic_gui on Mac), or run fsl and press the MELODIC button.

Before calling the GUI, you need to prepare each session's data as a 4D NIFTI or Analyze format image; there are utilities in fsl/bin called fslmerge and fslsplit to convert between multiple 3D images and a single 4D (3D+time) image.

Structural images for use as "highres" images in registration should normally be brain-extracted using BET.

 

 

 

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GUI details

Misc

Balloon help (the popup help messages in the MELODIC GUI) can be turned off once you are familiar with the GUI.

The Progress watcher button allows you to tell Melodic not to start a web browser to watch the analysis progress. If you are running lots of analyses you probably want to turn this off; you can view the same logging information by looking at the report_log.html or log.txt files in any MELODIC directories instead. 

Data

First, set the filename of the 4D input image (e.g. /users/sibelius/origfunc.nii.gz) by pressing Select 4D data. You can select multiple files if you want MELODIC to perform a group analysis or if you want to run separate ICAs with the same setup. Results for each input file will be saved in separate .ica directories, the name of which is based on the input data's filename (unless you enter an Output directory name).

Delete volumes controls the number of initial FMRI volumes to delete before any further processing.

TR controls the time (in seconds) between scanning successive FMRI volumes. Changes here will not affect the analysis and only change the x-axis units of the final time series plots.

The High pass filter cutoff controls the longest temporal period that you will allow.

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Pre-Stats

Low-frequency drifts and motion in the data can adversely affect the decomposition. In most cases, you would want to motion-correct the data, remove these drifts first or perform other types of typical data pre-processing before running the analysis. This can be done from within the Melodic GUI Pre-stats section.

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