Obtaining the code
Brain-view is hosted at launchpadgithub: https://launchpadgithub.netcom/sghanavati/brain-viewview2 Go to the downloads Downloads section of that website to get the latest release, or, to stay most up to date, get the source code directly from Bazaar github (the version control system):
bzr branch lp:~jason.lerch/brain-view/main git init git remote add origin email@example.com:sghanavati/brain-view2.git git pull -u origin master
To build brain-view you will need:
- Qt version 4.x (development was done against 4.5, but seems to work on 4.4 and 4.3 as well).
- Coin 3.0. (http://coin3d.org - Coin 2.5 might also work with brain-view, but this has not been tested yet).
- Quarter (http://coin3d.org/lib/quarter/releases/1.0.0)
- MINC version 2.x, bicpl, and oobicpl (http://packages.bic.mni.mcgill.ca/tgz/)
- boost_1.48.0 or higher (http://www.boost.org/users/download/)
- hdf5-1.8.6 or higher (http://www.hdfgroup.org/HDF5/release/obtain5.html)
brain-view is built using Qt's qmake. The basic steps are the following:
qmake MINCDIR=/path/to/minc QUARTERDIR=/path/to/quarter brain-view2.pro make
On Linux you will then have a binary called brain-view2 which can be copied where other such binaries live. On OS X you then have an application bundle that can be moved to the Applications folder.
Below is a screenshot of brain-view in action:
There are three main areas to the application: area (1) is the rendering area, area (2) a hierarchical list detailing all of the surfaces and associated files, and area (3) containing properties associated with each item in the hierarchical list. In the example above two surfaces (left and right hemisphere for the same subject in this case) have been loaded, resulting in two geometry scenes visible in area (2). Below each geometry-scene is an entry for the surface itself - clicking on it will allow one to change the colour and opacity in the property window (the left surface having been set to an opacity of 0.75 in the above example). The right surface also has a vertstats file opened, which in this case contains a single column (Column0) describing the cortical thickness. Clicking on each column will cause that column to be mapped onto the surface using the colourmap shown in the property area. Different ranges for the colour mapping can be chosen by entering the desired values in the upper and lower range text boxes, and different colourmaps are selectable from the drop-down box.