brainbow

Script for visualizing ICA/ROI brain parcellation

Requirements

pip install brainbow

Examples

brainbow -n {your_brain_map}.nii

Quick guide

• provide a path to nifti map (-n/--nifti flag) and anatomical underlay (-a/--anat flag, optional)
• control the output with --sign, --thr, and --no-norm flags
• to plot only certain components use -c/--component flag
• to set cut coordinates manually use --cut flag
• see below for more info

Options for brainbow

• -n/--nifti

  • path to the nifti file with 4D ICA map to convert to images (last dimension is components), or
  • path to the nifti file with 3D ROI map to convert to images (int values from 0 to n_regions);
  • required

• -a/--anat

  • path to the anatomical image to use as an underlay
  • if none is provided, the MNI 152 template is used as an underlay

• -o/--output

  • name of the output file(s)
  • default - brainbow-output.png/svg
  • You can specify the exact extension (png or svg). If none is provided, files with both extensions will be created

• --rich

  • if --rich is passed, in addition to the basic output a config file and a csv file containing cut coordinates is generated

• -s/--sign

  • choices: pos, neg, both
  • used for leaving only positive (pos), only negative (neg), or all values (both) in the components
  • ALSO controls the colormap

• --thr

  • threshold value for component significance
  • if component is significant, thr is used to mask values: -thr < value < thr
  • if all abs values in the component are below thr, component won't be visualized
  • default - 0.2

• --no-norm

  • use to disable data normalization
  • normalization includes:
    • centering around median,
    • divsion by the max abs value, and
    • divsion by the sign (1 or -1) of this max abs value

• --extend

  • if passed, in addition to overlay+underlay picture each component
    will also have a row with separate overlay/underlay
  • helpful for QC

• --dpi

  • dpi for png output
  • default - 150

• --annotate

  • choices: none, minimal, full
  • show components indices (minimal), components indices and cut coordinates (full), or nothing (none) on the output figure
  • default - minimal

• -c/--components

  • allows to provide a list of components to plot (e.g., '42 4 2')
  • enumeration starts with 1

• --cut

  • allows to set the cut coordinates manually
  • default behavior is to use the coordinates of the max abs value of each component
  • needs to be either:
    • a path to scv file (like the one created by --rich flag), or
    • a comma separated list of 3 cooridnates, which will be used for all components.
  • coordinates order should be RAS+
  • be careful when using with --components flag: brainbow assumes that the components order in the csv file correspond to the order of the provided components

Output example