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

Quickstart

Install murfi from a pre-built docker image:

sudo singularity build -F murfi.sif docker://ohinds/murfi:latest

This command will take some time, as it downloads a pre-built murfi docker image from dockerhub, then builds a singularity image (murfi.sif) from the docker image.

Running the example

mkdir murfi_example_data && \
    cd murfi_example_data && \
    curl -fsSL https://www.dropbox.com/s/1vvrz2g4tbzoh5c/murfi_example_data.tgz | tar -xz --strip-components 1
MURFI_SUBJECTS_DIR=.. MURFI_SUBJECT_NAME=murfi_example_data singularity exec ../murfi.sif murfi -f scripts/neurofeedback.xml

In another terminal:

cd murfi_example_data/scripts
singularity exec ../../murfi.sif ./servedata.sh 3000 15000 $(hostname)

Development

Dependencies:

1. libace
2. freeglut
3. libgsl
4. vxl
5. qt5
6. libniftiio

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

sudo apt-get install \
    build-essential \
    curl \
    cmake \
    libace-dev \
    libgsl-dev \
    libnifti-dev \
    libboost-filesystem-dev \
    qtbase5-dev \
    qtchooser \
    qt5-qmake \
    qtbase5-dev-tools \
    libqt5opengl5-dev

To install vxl, use the following commands:

curl -fsSL https://github.com/vxl/vxl/archive/v3.5.0.tar.gz | tar xz --strip-components 1 \
    && mkdir build \
    && cd build \
    && cmake -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/usr .. \
    && make -j 4 \
    && sudo make install \
    && rm -rf build \
    && ln -s /usr/include/vxlinclude/vxlcoreinclude/vxlvnl/ /usr/include/vxlinclude/vxlcoreinclude/vnl

Compilation:

cd <path to toplevel murfi directory>
make -j$(nproc)

Installation (optional):

sudo ln -sf bin/murfi /usr/bin

Funding

This project was partially funded by several sponsors:

• DARPA
• NIH
• McGovern Institute Neurotechnology Development Grant