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Compressed Sensing and Motion Correction LAB: An MR acquisition and reconstruction system

Home Page: https://sites.google.com/site/kspaceastronauts

License: Other

C++ 23.25% MATLAB 55.38% M 0.07% Makefile 0.04% C 18.50% Shell 0.01% Fortran 1.66% CMake 0.64% Java 0.38% Mathematica 0.01% Dockerfile 0.08%

mri compressed-sensing motion-correction siemens gadgetron matlab cs-moco-lab

cs_moco_lab's Introduction

CS_MoCo_LAB

Compressed Sensing and Motion Correction LAB: An MR acquisition and reconstruction system

Generate a Compressed Sensing (CS) accelerated MR sequence and reconstruct the acquired data online on the scanner by means of Gadgetron or offline on an external workstation.

Acquistion

Generic subsampling class for Compressed Sensing acquisitions
CS accelerated gradient echo sequence (2D, 2D+time, 3D, 3D+time): CS_FLASH (Siemens, VB20P)
MR motion imaging sequence (4D, 5D): CS_Retro (Siemens, VB20P, VE11C, VE11P)

Reconstruction

CS and motion-resolved reconstruction system for Gadgetron (C++)
CS reconstruction system in Matlab (including a GUI)

Applications

acquisition: CS_Retro (Siemens, VB20P, VE11C, VE11P)
reconstruction: CS_LAB in gadgetron + data emitters and injectors

Image Registration

https://sites.google.com/site/kspaceastronauts/motion-correction/mocogui

Installation

More information: https://sites.google.com/site/kspaceastronauts/compressed-sensing/cslab#TOC-Prerequisites

Gadgetron

standalone

git clone https://github.com/thomaskuestner/CS_MoCo_LAB.git
mkdir build
cd build
cmake ../
make
sudo make install

docker

docker pull kspaceastronauts/cs_moco_lab
docker run -it --volume $(pwd):/opt/data kspaceastronauts/cs_moco_lab

Matlab

git clone https://github.com/thomaskuestner/CS_MoCo_LAB.git
cd CS_MoCo_LAB/matlab/CS_LAB_GUI
matlab CS_LAB_GUI

References

MR-based respiratory and cardiac motion correction for PET imaging.
Medical Image Analysis, 2017.
Thomas Küstner, Martin Schwartz, Petros Martirosian, Sergios Gatidis, Ferdinand Seith, Christopher Gilliam, Thierry Blu, Hadi Fayad, Dimitris Visvikis, F. Schick, B. Yang, H. Schmidt and N.F Schwenzer.
[doi] [BibTeX] [Endnote]

Compressed Sensing LAB: An MR acquisition and reconstruction system.
Proceedings of the ISMRM Workshop on Data Sampling and Reconstruction. Sedona, AZ, USA, 2016.
Thomas Küstner, Martin Schwartz, Christian Würslin, Petros Martirosian, Nina F. Schwenzer, Bin Yang and Holger Schmidt.
[BibTeX] [Endnote]

Image Reconstruction System for Compressed Sensing Retrospective Motion Correction for the Application in Clinical Practice.
Proceedings of the International Society for Magnetic Resonance in Medicine (ISMRM). Singapore, 2016.
Martin Schwartz, Thomas Küstner, Christian Würslin, Petros Martirosian, Nina F. Schwenzer, Fritz Schick, Bin Yang and Holger Schmidt.
[BibTeX] [Endnote]

Please read LICENSE file for licensing details.

Detailed information and installation instructions are available at:
https://sites.google.com/site/kspaceastronauts/compressed-sensing/cslab

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cs_moco_lab's Issues

CS_LAB library not found by Gadgetron with RegistrationGadget

When the CS_LAB is compiled with RegistrationGadget (CMakeLists.txt lines 339 & 374), Gadgetron is not able to find the library. Commenting these lines out solves the problem (but cannot be the fix, obviously). See also commit 3c313ae.

IceGadgetron VB20P

Hello,

I try to install CS_LAB package on mMR scanner with IDEA VB20P. I download "IceGadgetron" for VB17 from IDEA community website, and fixed some lines to compile but all failed. I wonder if k-Space Astronauts group has a working version of IceGadget source code on VB20P. Could you share? Many thanks.

Chan

CMakeLists.txt for compiling 'subsampling.exe' on ubuntu 14.04

---------------------------

The code for 'subsampling.exe' can be compiled easily.

This CMakeLists.txt is provided just for easier on Ubuntu 14.04.

project(subsampling)

cmake_minimum_required(VERSION 2.8)

set(include_file Approx.h LinkedList.h Point.h SomeFunctions.h VariableDensity.h VDSamplingUpper.h SubsampleMain.h)
set(src_file Approx.cpp LinkedList.cpp Point.cpp SomeFunctions.cpp VariableDensity.cpp VDSamplingUpper.cpp SubsampleMain.cpp)
set(CMAKE_INSTALL_PATH ${CMAKE_HOME_DIRECTORY})

add_executable(subsampling ${src_file} ${include_file})

install(TARGETS subsampling RUNTIME DESTINATION ${CMAKE_INSTALL_PATH})

How to get a .mat file desired by the CS_LAB_GUI program from a .dcm file ?

Hello， I have many .dcm files, and I want to use these files to test the CS_LAB_GUI program. But when I translate the .dcm file to the .mat file desired by the program, it returns error when loading. Am I missing something. The following is the code for translating .dcm to .mat.

%% 读取数据
filename = 'xx.dcm';
dcm = dicomread(filename);
info = dicominfo(filename);
dcm = double(dcm); % 转为double方便后续处理

%% 归一化处理（此处也可直接使用mat2gray()函数）
lv = min(dcm(:));
uv = max(dcm(:));
dcmIM = (dcm - lv)/(uv - lv);

dcmMat.kSpace ={complex(dcmIM)}
dcmMat.measPara.dim = [size(dcmIM,1), size(dcmIM,2), 1, 1, 1]
dcmMat.measPara.LCall = [1,1,1,1]
dcmMat.measPara.dimension = '2D'

ktFOCUSS2DT.m line 133: d may be modified to d_old ?

Hi,

Thank you for sharing CS_LAB.

I tried MATLAB version for 2DT recon, and encountered an error about missing 'd_old'. Maybe the 'd' variable @ line 133 in ktFOCUSS2DT.m should be changed to 'd_old'.

Moreover, is it possible to recompiled the CS_LAB_Gadget library for Gadgetron on Linux (ubuntu 14.04 LTS) , that is changing from .dll/.lib file to .so file)? Would you please to show me how much CS_LAB_Gadget (C++) is open sourced ? We are working on implementing an improved 2DT recon (k-t ISD) based on k-t FOCUSS, and wish to start from CS_LAB_Gadget if possible.

Thank you again.
Best wishes,
Jia Sen

A matlab script aims to simplify reading mask generated by subsampling.exe

This matlab script call the subsampling.exe in MATLAB via system call, and read generated mask in subsamplingpatter.txt to MATLAB. Also, the Point Spread Function of ESPReSSo mask is displayed.
Note: the PSF calculation may be different from the one used by the authors of ESPReSSo. I could not reproduce the PSF in Fig.2 in the paper of ESPReSSo.

Just rename the upload .txt file to .m file.
ESPReSSomask_in_matlab.txt

Compatibility check

@F462 Can you please confirm that LAP Gadget and PCA-based self-navigation signal extraction are working properly in new Gadgetron version?

no fCreateLoopImages in repository

This function is called twice in ktFOCUSS4DMotion.m (lines 147 and 279), but it does not seem to exist anywhere in the repository. Can you please upload this file?