knorrfg / conview

a specialized nifti viewer

Conview

Usage

This is Conview, a tool to get an intuitive grasp of your connectivity matrices. To view the connectivity of a region on the right side, hold control while you click on the Region on the Left side.

You need two files to use this program:

1. A 4D nifti, which holds all the images that are represented by one column in your connectivity matrix.
2. A 3D Atlas nifti file, which for each region has the value that implies the index in the forth dimension of the 4D nifti. At that index, the 4D nifti should contain a 3D volume that displays the connectivity of the region in the atlas image with the rest of the brain.

If you have those two images, just start the program by typing conview <atlas file path> <4d nifti file path> into the command line

List of Hotkeys: (all changes will apply to the side you clicked on last, left if you havent clicked yet)

t: set threshold
m: change color map
i: change vmin
a: change vmax
v: reset vrange to default
g: toggle location and value information
h: show help

Installation

Conview is written in Python and requires version 3.9. If you have it installed, you can install conview by typing

pip install git+https://github.com/KnorrFG/conview.git

into your command line. This method of installation requires git.