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 People

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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.

Create Separate Logs for Each Run

It would be useful if murfi could output separate logs each time it is run rather than append one after the other in a single log.

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.

difference of ROIs

is there a way to implement a difference of roi value calculation? when one roi is background/wm it's variance could be low and hence z value can be really high. subtracting z values makes sense only if one is comparing task related rois.

in the other cases, one might want to z-ify the difference in activity between two mask regions.

servenii and servenii4d

with the current qtmurfi minimal configuration modifed to save images:

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

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

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...

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.

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

roi values - why two?

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

display shaded region for error estimation

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