Skip to content

Latest commit

 

History

History
78 lines (70 loc) · 3.16 KB

README.md

File metadata and controls

78 lines (70 loc) · 3.16 KB
Raw

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