Script for visualizing ICA/ROI brain parcellation
Project description
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
flag) and anatomical underlay (-a
flag) - control the output with
--sign
,--thr
, and--norm/--no-norm
flags - to plot only certain components use
-c
flag - see below for more info
Options for brainbow
-
--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
-
--anat
- path to the anatomical image to use as an underlay
- required
-
--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
-
--dir
- directory for saving results
- can be nested (e.g.,
final/most_final
) - default - directory where brainbow is executed
-
--sign
- choices:
pos, neg, both
- used for filtering only positive, only negative, or all values in the components
- ALSO controls the colormap
- default -
both
- choices:
-
--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
- whether the components from nifti should be normalized:
-
--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
- If
-
--dpi
- dpi for png output
- default -
300
-
--annotate/--no-annotate
- If
True
, enumerate components in the output figure - default -
True
- If
Output example
Project details
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