brainbow 0.1.6

Script for visualizing ICA/ROI brain parcellation

brainbow

Script for visualizing ICA/ROI brain parcellation

Requirements

pip install brainbow

Examples

brainbow --nifti nifti.nii --anat anat.nii 

Quick guide

• provide path to nifti map (-n/--nifti flag) and anatomical underlay (-a/--anat flag)
• control the output with --sign, --thr, and --norm/--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
  • required

• -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, both extensions will be used

• --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 filtering only positive (pos), only negative (neg), or all values (both) in the components
  • ALSO controls the colormap
  • default - both

• --thr

  • threshold value for component significance
  • if component is significant, thr is used to mask values: -thr < value < thr
  • default - 0.3

• --norm/--no-norm

  • whether the components from nifti should be normalized:
    • z-scored,
    • divided by the max abs value, and
    • divided by the sign (1 or -1) of this max abs value.
  • may produce a better looking picture, but not recommended for QC
  • default - True

• --extend/--no-extend

  • If True, in addition to overlay+underlay picture each component
    will also have a row with separate overlay/underlay
  • helpful for QC
  • default - False

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

Output example