gablab / murfi2 Goto Github PK

The realtime fMRI software platform - an MIT-MGH collaboration

Home Page: http://mindhive.mit.edu/realtime/

License: Other

Shell 0.70% Makefile 1.04% C++ 57.71% C 17.95% MATLAB 1.80% Python 0.94% Jupyter Notebook 19.68% Dockerfile 0.06% Cython 0.12%

murfi2's Introduction

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:

libace
freeglut
libgsl
vxl
qt5
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

murfi2's People

Contributors

Stargazers

Watchers

Forkers

satra ohinds cccbauer nagyistge pwighton kaczmarj guruevi

murfi2's Issues

license compatibility

@ohinds - we need to ensure that all dependent libraries are either BSD/MIT/Apache for murfi2 to be released as apache. i see that we are linking to gsl, which would prevent murfi2 from being released under apache v2.

roi values - why two?

for every mask murfi appears to return two values for each TR. what are these two values?

config file minimal requirements

the qt branch minimal config file is not minimal.

the xml file needs a few more things amongst others:

disabled=false
port number
receiveimages=true

also, the config file requires the subject info for murfi to load it, even if environment variables are set.

Path to QColor

The call to QColor in the PlotController.h file during installation doesn't work... I have the latest Qt update, and the QColor file is in /usr/include/x86_64-linux-gnu/qt5/QtGui. Compiler says there is no QColor file or directory...

display shaded region for error estimation

Using servenii to send data

Hey,

I am trying to use servenii to send nifti files to a vagrant box running murfi to visualize fMRI data to test the real time analysis. The issue we are having now is that the data in the murfi window looks scrambled. When the nifti file is opened with fsleyes, the labels are also incorrect. Is this a problem with the real time fMRI ICE Configurator sending data to the computer, or is the issue with servenii?

Thanks in advance,
Arun Venkataraman

new open header erroring

i was testing the open header with andre today at mit. and was running into this error. didn't have time to debug.

received info
processing 616 header data bytes
header received: TR=10
Requires: 294912 bytes
ExternalImageHeader(magic='ERTI', headerVersion=4, seriesUID='1.3.12.2.1107.5.2.32.35115.2013081322103941796402114', scanType='EPI', imageType='3D', note='Initial OpenHeader Implementation. repetitionDelayMS is currently hard-coded to 0', dataType='int16_t', isLittleEndian=True, isMosaic=True, pixelSpacingReadMM=3.28125, pixelSpacingPhaseMM=3.28125, pixelSpacingSliceMM=4.0, sliceGapMM=1.0, numPixelsRead=64, numPixelsPhase=64, numSlices=30, voxelToWorldMatrix=[-3.28125, 0.0, 0.0, 105.0, 0.0, -3.28125, 0.0, 105.0, 0.0, 0.0, 5.0, -72.5, 0.0, 0.0, 0.0, 1.0], repetitionTimeMS=2000, repetitionDelayMS=0, currentTR=10, totalTR=10, isMotionCorrected=True, mcOrder='TZYX', mcTranslationXMM=-0.0094293402949011, mcTranslationYMM=0.0008725363597534, mcTranslationZMM=0.014861163666259001, mcRotationXRAD=-0.0048493300566949, mcRotationYRAD=0.0055316874022655, mcRotationZRAD=-0.000439865096032)
----------------------------------------
Exception happened during processing of request from ('192.168.2.3', 54797)
Traceback (most recent call last):
  File "/software/anaconda/envs/devpype/lib/python2.7/SocketServer.py", line 593, in process_request_thread
    self.finish_request(request, client_address)
  File "/software/anaconda/envs/devpype/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "receive_nii.py", line 35, in createHandler
    return ThreadedTCPRequestHandler(callback, infoclient,  *args, **keys)
  File "receive_nii.py", line 23, in __init__
    SocketServer.BaseRequestHandler.__init__(self, *args, **keys)
  File "/software/anaconda/envs/devpype/lib/python2.7/SocketServer.py", line 649, in __init__
    self.handle()
  File "receive_nii.py", line 26, in handle
    self.callback(self.infoclient, self.request)
  File "receive_nii.py", line 40, in process_data_callback
    infoclient.process_data(sock)
  File "receive_nii.py", line 126, in process_data
    (self.ei.get_image_size(), len(img_data))
ValueError: Image data wrong size: expected 294912 bytes, got 8688

also for some reason hdr.seriesUID is changing in subsequent TRs

ExternalImageHeader(magic='ERTI', headerVersion=4, seriesUID='1.3.12.2.1107.5.2.32.35115.2013081322103941796402114', scanType='EPI', imageType='3D', note='Initial OpenHeader Implementation. repetitionDelayMS is currently hard-coded to 0', dataType='int16_t', isLittleEndian=True, isMosaic=True, pixelSpacingReadMM=3.28125, pixelSpacingPhaseMM=3.28125, pixelSpacingSliceMM=4.0, sliceGapMM=1.0, numPixelsRead=64, numPixelsPhase=64, numSlices=30, voxelToWorldMatrix=[-3.28125, 0.0, 0.0, 105.0, 0.0, -3.28125, 0.0, 105.0, 0.0, 0.0, 5.0, -72.5, 0.0, 0.0, 0.0, 1.0], repetitionTimeMS=2000, repetitionDelayMS=0, currentTR=7, totalTR=10, isMotionCorrected=True, mcOrder='TZYX', mcTranslationXMM=0.0042315309944431, mcTranslationYMM=-0.0025443566414593, mcTranslationZMM=0.0071906872163449, mcRotationXRAD=-0.0025820459857879, mcRotationYRAD=-0.0049068081238989, mcRotationZRAD=0.0008466105930182)
----------------------------------------
received info
processing 616 header data bytes
header received: TR=8
Requires: 294912 bytes
ExternalImageHeader(magic='ERTI', headerVersion=4, seriesUID='1.3.12.2.1107.5.2.32.35115.2013081322103945048702115', scanType='EPI', imageType='3D', note='Initial OpenHeader Implementation. repetitionDelayMS is currently hard-coded to 0', dataType='int16_t', isLittleEndian=True, isMosaic=True, pixelSpacingReadMM=3.28125, pixelSpacingPhaseMM=3.28125, pixelSpacingSliceMM=4.0, sliceGapMM=1.0, numPixelsRead=64, numPixelsPhase=64, numSlices=30, voxelToWorldMatrix=[-3.28125, 0.0, 0.0, 105.0, 0.0, -3.28125, 0.0, 105.0, 0.0, 0.0, 5.0, -72.5, 0.0, 0.0, 0.0, 1.0], repetitionTimeMS=2000, repetitionDelayMS=0, currentTR=8, totalTR=10, isMotionCorrected=False, mcOrder='TZYX', mcTranslationXMM=0.0, mcTranslationYMM=0.0, mcTranslationZMM=0.0, mcRotationXRAD=0.0, mcRotationYRAD=0.0, mcRotationZRAD=0.0)

so this breaks the assert.

servenii: command not found

Hi Satra,

I installed murfi afresh on a new laptop but am getting

servenii: command not found

when trying to run the `./servedata.sh' script

servenii not sending appropriate data information - murfi doesn't show a mosaic
servenii4d works as in murfi shows a mosaic and the rois on it

in neither case above does murfi save the data with proper voxel information - i believe this is an issue with the two scripts above rather than murfi as murfi saves data from the scanner properly.

with servenii, it does this:

$ mri_info img-00020-00001.nii 
Volume information for img-00020-00001.nii
          type: nii
    dimensions: 12 x 12 x 31
   voxel sizes: 3.0000, 3.0000, 3.6000

with servenii4d it does this:

$ mri_info img/img-00021-00001.nii 
WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent
   (0,1.00007) (0,1.01065) (3.6,0.992484) 
This is probably due to shear in the vox2ras matrix