Motion compensation for

PET-MR applications

Christoph Kolbitsch

Overview

Gadget

Gadget

Gadget

Gadget

Gadget

Gadget

Gadget

Gadget

• Read data

• Remove oversampling in readout

• Apply k-space filter

• Transform k-space data to image space

• Read from raw matrix

• Conversion to uint

• Save data to hdf5

XML

Overview - filterRecon

• Read data

• Remove oversampling in readout

• Convert to uint

• Save data to hdf5

• Apply k-space filter

• Transform k-space data to image space

Gadgetron

Matlab

XML

filterRecon.m

filterRecon

Matlab

• Read data

• Remove oversampling in readout

• Apply k-space filter

• Transform from k-space to image space

Gadgetron

Matlab

• Define data and parameter files

• Receive image data

• Postprocessing

Matlab

Hypothetical PET-MR Compensation for MR motion

convert toISMRMRDk-space++

gadget 1

gadget

STIR

raw

ISMRMRD image or DICOM

[Image: Hartford Hospital]

other dataList mode / sinograms

gadget N

PET derived motion signal

DEMO: Applying Motion to MRI

gadget 1

gadget

ISMRMRD image or DICOM

ISMRMRDinspector

MATLABcode

gadget N

Modify recon to apply motion “correction” phases to k-space.(15mm translation, half-way through acquisition)

𝒆−𝟐𝝅𝒊𝒌∆𝒙

ISMRMRD file: simple_gre.h5Config: matlab_moco.xml

explore_h5.m

Iterative reconstruction

• Read data

• Remove oversampling in readout

• Reconstruct using GPU SENSE

• Convert and save data to hdf5

• Calculate k-space trajectory, dcf, csm,

regularisation,....

Gadgetron

Matlab

Iterative reconstruction

Iterative reconstruction

Gadgetron

Matlab

MatlabBufferGadget.cpp

Iterative reconstruction

Matlab

Gadgetron

MatlabBufferGadget.cpp

Iterative reconstruction

gpuRadialPrepGadget.cpp

Prep

SENSE

SPIRIT

Python

Python Notebook

‘Live’ code, run in cells.

Similar to running cells in MATLAB.

Jupyter Notebook