murfi2: A C++ repository from ohinds

MURFI (multivariate and univariate real-time functional imaging) is a software package for real-time processing of functional brain images for neuroscience applications. At the moment murfi is fMRI-centric, but we plan to add support for other imaging modalities.

This is an open-source release of the MURFI platform (see LICENSE for details).

For using MURFI with Siemens scanners, a proprietary data transfer sequence can be obtained via a C2P agreement. Alternatively, for non-Siemens scanners or for your own Siemens functors, Murfi will accept data over TCPIP conformant with the following structured information:

https://github.com/gablab/murfi2/blob/master/src/io/RtExternalSenderImageInfo.h

If you use MURFI in your own research, please cite:

Oliver Hinds, Satrajit Ghosh, Todd W Thompson, Julie J Yoo, Susan Whitfield-Gabrieli, Christina Triantafyllou, John D E Gabrieli (2011) Computing moment-to-moment BOLD activation for real-time neurofeedback. Neuroimage 54: 1. 361-368 Jan

http://dx.doi.org/10.1016/j.neuroimage.2010.07.060

Installation

Dependencies:

libace-dev
freeglut3-dev
libgsl0-dev
libxi-dev
libxmu-dev
vxl
qt5
libniftiio

On recent Ubuntu distros, the following command will install all dependencies:

$ sudo apt-get install build-essential libace-dev freeglut3-dev libgsl0-dev cmake libxi-dev libxmu-dev libboost-filesystem-dev libnifti-dev nifti-bin libqt4-dev libqwt-dev libvtk5-qt4-dev libvxl1-dev qt5-default libqt5*-dev

Compilation:

$ cd <path to toplevel murfi directory>
$ make -j 8

Installation (optional):

$ sudo ln -sf bin/murfi /usr/bin

Running the example

$ wget https://www.dropbox.com/s/1vvrz2g4tbzoh5c/murfi_example_data.tgz
$ tar -xzvf murfi_example_data.tgz
$ export MURFI_SUBJECTS_DIR=$PWD
$ export MURFI_SUBJECT_NAME=murfi_example_data
$ murfi -f murfi_example_data/scripts/neurofeedback.xml

In another terminal:

$ cd murfi_example_data/scripts
$ ./servedata.sh

Using Vagrant

Download and install Vagrant and VirtualBox. Then download this archive. Requires an X-server installed locally.

Unzip the archive and using a terminal change to the unzipped directory.

$ vagrant up
$ vagrant -X ssh
$ cd /vagrant
$ source murfi_vagrant.sh
$ make -j2 # first time only to compile murfi

Then follow the [Running the example] section above.

On another terminal from the same unzipped directory do:

$ vagrant ssh
$ cd murfi_example_data/scripts
$ ./servedata.sh

Funding

This project was partially funded by several sponsors:

DARPA
NIH
McGovern Institute Neurotechnology Development Grant

ohinds/murfi2