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brain-view

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Table of Contents

Overview

Brain-view is designed to visualize bits of geometry - such as meshes representing the cortical surface, line objects representing the centre line of vessels, or connected cylinder objects representing segmented vasculature - along with associated information, such as cortical thickness at every vertex, statistical maps, labels of vessel segments on every cylinder, etc. It is based on Coin (Inventor), Qt, and the various MINC file formats.

 WhatWhat's new in version 2?

Version 2 is a complete rewrite of brain-view. The main motivation were to be able to deal with multiple objects, such as left and right surfaces, etc., and in the process clean up some of the cruft that had accumulated in the previous code-base. Not all features of brain-view 1 are included - there's no interaction with R, no painting ability, etc. All that is planned, however. For the moment only use brain-view2 if you want to experiment with it and help with the testing.

 Obtaining Obtaining the code

Brain-view is hosted at github: https://github.com/sghanavati/brain-view2 Go to the Downloads section of that website to get the latest release, or, to stay most up to date, get the source code directly from github (the version control system):

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 Building Building brain-view

brain-view is built using Qt's qmake. The basic steps are the following:

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(See also the end of this page for more details).

 Using Using brain-view

Start brain-view by double clicking on the brain-view2 icon or entering it on the command line. If started from the command line, it can take an arbitrary number of filenames corresponding to obj files (polyhedra or line at the moment), files associated with the obj files (.txt or .vertstats files), tag files, hdf5 files (.h5 files are created by vessel tracking code and post-processed into hdf5 database format. In order to successfully read these files into brain-view, required groups and datasets should exist in the file. more detail will be provided below), and configuration files (.config providing the numerical and anatomical labels and their corresponding RGB colors) . The order of the filenames matter, since .txt/.vertstats files have to follow the geometry file with which they are associated. Files can also be opened through the file menu once the application has started.

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If any bit of the scene is clicked on in the rendering area the information in the hierarchical list will update with the values at the selected location. You might have to scroll to the right in the hierarchical list to see it. Also note that the hierarchical list can be detached from the main window by selecting and dragging it (where it says "Resources") away from the main window. It can be redocked later through the same process.

Discrete Template Colormap for CIVET AAL Atlas

If you are using the CIVET-1.1.12/models/AAL_atlas_left.txt and CIVET-1.1.12/models/AAL_atlas_right.txt files, there is a discrete unique-color bar here. This allows for nice clear labeling of a CIVET object in brain-view2. Intensity range must be set from 0-91 to work properly with the surface atlas. (Thanks Gabriel Devenyi for providing the color bar. It was generated using http://tools.medialab.sciences-po.fr/iwanthue/ + matplotlib + gimp.)

Installation

In order to install brain-view on Mac OSX mountain lion you will need to take the following steps. The installation on a Linux-based OS such as ubuntu will follow similar steps but probably with less headache!

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