https://github.com/dangom/icicle-tree-melodic

Icicle tree to visualize the variance explained by each IC component, as output from MELODIC.
https://github.com/dangom/icicle-tree-melodic

fsl melodic neuroimaging

Last synced: about 1 month ago
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Icicle tree to visualize the variance explained by each IC component, as output from MELODIC.

• Host: GitHub
• URL: https://github.com/dangom/icicle-tree-melodic
• Owner: dangom
• License: gpl-3.0
• Created: 2017-06-18T22:10:08.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-07-12T13:48:32.000Z (over 7 years ago)
• Last Synced: 2023-10-05T20:31:21.409Z (about 1 year ago)
• Topics: fsl, melodic, neuroimaging
• Language: Python
• Size: 34.2 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.org
  • License: LICENSE

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README

        
#+TITLE: ICA Icicle Plots

#+AUTHOR: Daniel Gomez

#+DATE: 11.07.2017

A tool to generate icicle plots displaying:

1. The amount of variance in each ICA component;

2.  The amount of variance explained by the dimensionality of the ICA decomposition, in comparison to the full data;

3. Components accepted and rejected by either FIX or ME-ICA cleaning (the only currently supported methods).

Here is an example image:

[[./icicle_plot.png]]

The upper row shows the variance not explained (in orange) by the space spanned by the ICA components, but present in the original data nonetheless.

The lower row shows components that are accepted (in blue) by the cleaning method, and rejected (in orange). Each rectangle represents one component, and its area is equivalent to the amount of variance it explains.

** Usage

ICA Icicle Plots currently supports FIX and ME-ICA. It will automatically detect what cleaning method was used, if any.

However, if you did use FIX, you'll have to specify the FIX results.txt file yourself. This file usually has a name similar to "fix4melview_blabla.txt".

Directly from the help menu:

#+begin_quote

icicles.py [-h] [--fix FIX] i o

Save an icicle plot to file

positional arguments:

  i           The input ICA directory

  o           The output filename

optional arguments:

  -h, --help  show this help message and exit

  --fix FIX   If FIX, the txt containing fix classification results

#+end_quote

** Installation

Clone the repository.

** Dependencies

Python3 with pandas and matplotlib.