smistad / tube-segmentation-framework

A software for fast segmentation and centerline extraction of tubular structures (e.g. blood vessels and airways) from different modalities and organs using GPUs and OpenCL

Tube Segmentation Framework

The tube segmentation framework is a software for fast segmentation and centerline extraction of tubular structures (e.g. blood vessels and airways) from different modalities (e.g. CT, MR and US) and organs using GPUs and OpenCL.

For details about the implementation see the following publication:
GPU accelerated segmentation and centerline extraction of tubular structures in medical images
Erik Smistad, Anne C. Elster and Frank Lindseth
International Journal of Computer Assisted Radiology and Surgery
2013

If you use this software in any publications, please cite our article.

See the file LICENSE for license information.

Dependencies

• OpenCL. You need an OpenCL implementation installed on your system to use this software (AMD, NVIDIA, Intel or Apple)
• Boost iostreams. E.g. on Ubuntu linux use the following package: libboost-iostreams-dev
• The two submodules: SIPL and OpenCLUtilities
• GTK 2 for visualization (not required, used by the SIPL module). On Ubuntu linux use the following package: libgtk2.0-dev

Compiling

To compile the software first make sure that all software dependencies are installed and set up correctly. Next, use cmake.

For instance on linux, do the following:

cmake .
make -j8

Usage

To see the help message use the software with no arguments. ./tubeSegmentation

The first arguments is the dataset to process. This has to be a metadata (.mhd) file.

Some test data is available with the software. You can test the program with the following command:

./tubeSegmentation tests/data/synthetic/dataset_1/noisy.mhd --parameters Synthetic-Vascusynth --display

Parameters

This software has a lot of parameters and several parameter presets are available:

• Lung-Airways-CT
• Neuro-Vessels-USA
• Neuro-Vessels-MRA
• AAA-Vessels-CT
• Liver-Vessels-CT
• Synthetic-Vascusynth

The parameter preset is set with the program argument "--parameters ".

Tests

This software contains several tests written with Google Test. Install Google Test and run cmake again to compile the tests. Run the tests using the command ./tests/runTests

tube-segmentation-framework's Issues

how to can the ground truth data generation from centerlines by this program ?

i found in a paper that they used this method to generate labels from the centerline (cvs file ) , i am using the same data and i would like to use this method but i do not know how

Compile on windows

Does the code support compile on windows ?

Error occurred when compiling

Hello

When I compile this project. Error was occurred:

error C2664: 'oul::HistogramPyramid3DBuffer::HistogramPyramid3DBuffer(const oul::HistogramPyramid3DBuffer &)' : cannot convert argument 1 from 'OpenCL' to 'oul::Context &'

Source code is : oul::HistogramPyramid3D hp3(ocl);

That means, there is no conversion between oul::Context and OpenCL. I'm using the newest version OpenCLUtilityLibrary (master) and Tube-Segmentation-Framework (master). I'm wondering if I have a mismatched version.

Thank you very much.

two error occurred when I try to build this project on my mac

OS X 10.11.6
git clone --recurse-submodules https://github.com/smistad/Tube-Segmentation-Framework.git
cd Tube-Segmentation-Framework
cmake .
make -j8
Then I got this:

In file included from /Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Core.cpp:6:
/Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Core.hpp:762:15: error:
no matching constructor for initialization of 'SIPL::ConversionException'
...ConversionException("image size mismatch in assignment", LINE, FILE);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Exceptions.hpp:164:7: note:
candidate constructor (the implicit copy constructor) not viable: requires
1 argument, but 3 were provided
class ConversionException : public SIPLException {
^
/Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Exceptions.hpp:164:7: note:
candidate constructor (the implicit move constructor) not viable: requires
1 argument, but 3 were provided
/Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Exceptions.hpp:164:7: note:
candidate constructor (the implicit default constructor) not viable:
requires 0 arguments, but 3 were provided
In file included from /Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Core.cpp:6:
/Users/Leon/Developer/Tube-Segmentation-Framework/SIPL/Core.hpp:802:15: error:
no matching constructor for initialization of 'SIPL::ConversionException'
...ConversionException("volume size mismatch in assignment", LINE, FILE);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Bug in validation of numerical parameters

for instance --min-mean-tdf 0.4

The code support compiling on windows?

Can the code compile on windows?