medical image analysis

Hop over to PeerJ to read about the algoritm implemented in MIA that can be used for the segmentation of paleoantological material. The tool you are looking for is mia-3dsegment-local-cmeans. Many thanks to Chris J. Dunmore and Dr. Matthew M Skinner ... [More] at the School of Anthropology & Consservation at the University of Kent, UK, for getting me involved in this research. [Less]

This release brings just two small changes, one one hand a bug was fixed in mia-3dsegment-local-cmeans, and mia now compiled against boost version 1.65.

The new version provides a tool for symmetric fluid dynamic registration, some local-cmeans based segmentation tool, new image filters, and it adds compatibility for VTK-7 data IO. The new version can also be run from a docker image. In addition ... [More] the new version fixes a number of issues: [tickets:#129]: Move all optional parts to addons, [tickets:#167]: Add an alternative FastICA that is independend of IT++, [tickets:#191]: Use C11 integer data types to ensure constistent data sizes, [tickets:#192]: Replace lazy copying wit move semantics, [tickets:#193]: Make documentation tool and nipype interfaces compatible with Python 3, [tickets:#194]: Create a complete facate for XML handling and remove dependency from libxml++, and [tickets:#195]: Correct errors in Nifti s-form handling. [Less]

For the latest release now a Docker image is now available. This makes running mia-tools of the latest stable release on non-linux operating systems easy, In order to run the tools by using this image, Docker must be installed accordingly. ... [More] Running mia-tools via Docker on Windows On MS Windows, the disk on which the data is located that you want to process needs to be enabled for sharing. With this in place, any mia tool, e.g. to run binarize by using mia-2dimagefilter type the following commands into powershell: $path= Convert-Path . docker run -w /home/mia -v ${path}:/home/mia --rm ` gerddie/mia-tools:2.4.5 ` mia-2dimagefilter -i someinput.png -o someoutput.png binarize:min=30 The input and output path must all be relative to and below the current working directory. For directory delimiters you must use / as the strings are passed literal, and the docker image is running a lightweight Ubuntu/Linux installation. Also, you should avoid spaces in directory names, If you want to convert the above command into a powershell script, be aware that fro running these scripts you have to change the execution policy for running scripts and sign the script (I wouldn't recommend to set the policy to Unrestricted). The script would then look like this: $path= Convert-Path . docker run -w /home/mia -v ${path}:/home/mia -u mia --rm ` gerddie/mia-tools:2.4.5 $args Running mia-tools on Unix-like operating systems On Unix like systems with a working Docker installations the script to run any mia comand line tool is docker run -w /home/mia \ -v $(pwd):/home/mia \ -u mia --rm \ gerddie/mia-tools:2.4.5 $* The same limitations for file locations and no-whitespace in file and directoriy names apply. Happy image processing! [Less]

For the latest release now a Docker image is now available. This makes running mia-tools of the latest stable release on non-linux operating systems easy, In order to run the tools by using this image, Docker must be installed accordingly. ... [More] Running mia-tools via Docker on Windows On MS Windows, the disk on which the data is located that you want to process needs to be enabled for sharing. With this in place, any mia tool, e.g. to run binarize by using mia-2dimagefilter type the following commands into powershell: $path= Convert-Path . docker run -w /home/mia -v ${path}:/home/mia --rm ` gerddie/mia-tools:2.4.4 ` mia-2dimagefilter -i someinput.png -o someoutput.png binarize:min=30 The input and output path must all be relative to and below the current working directory. For directory delimiters you must use / as the strings are passed literal, and the docker image is running a lightweight Ubuntu/Linux installation. Also, you should avoid spaces in directory names, If you want to convert the above command into a powershell script, be aware that fro running these scripts you have to change the execution policy for running scripts and sign the script (I wouldn't recommend to set the policy to Unrestricted). The script would then look like this: $path= Convert-Path . docker run -w /home/mia -v ${path}:/home/mia -u mia --rm ` gerddie/mia-tools:2.4.4 $args Running mia-tools on Unix-like operating systems On Unix like systems with a working Docker installations the script to run any mia comand line tool is docker run -w /home/mia \ -v $(pwd):/home/mia \ -u mia --rm \ gerddie/mia-tools:2.4.4 $* The same limitations for file locations and no-whitespace in file and directoriy names apply. Happy image processing! [Less]

The paper summarizing the results of the cardiac motion compensation challange from STACOM 2014, in which the MIA software package took part, has been accepted for publication: Beau Pontre, Brett R. Cowan, Edward DiBella, Sancgeetha Kulaseharan ... [More] , Devavrat Likhite, Nils Noorman, Lennart Tautz, Nicholas Tustison, Gert Wollny, Alistair A. Young, and Avan Suinesiaputra, An Open Benchmark Challenge for Motion Correction of Myocardial Perfusion MRI , IEEE Journal of Biomedical and Health Informatics, DOI: 10.1109/JBHI.2016.2597145 [Less]

The paper summarizing the results of the cardiac motion compensation challange from STACOM 2014, in which the MIA software package took part, has been accepted for publication: Beau Pontre, Brett R. Cowan, Edward DiBella, Sancgeetha Kulaseharan ... [More] , Devavrat Likhite, Nils Noorman, Lennart Tautz, Nicholas Tustison, Gert Wollny, Alistair A. Young, and Avan Suinesiaputra, An Open Benchmark Challenge for Motion Correction of Myocardial Perfusion MRI , IEEE Journal of Biomedical and Health Informatics, DOI: 10.1109/JBHI.2016.2597145 [Less]

The development of MIA has reached a new milestone with the release of the version 2.4. One of the major changes is that MIA can now rely fully on the C++11 facilities for multi-threading, making it possible to remove it's dependencies on the Intel ... [More] threading building blocks. As a result MIA can now be compiled and run on many more architectures, specifically, it can now be build on all Debian release architectures. [Less]

The last few days I have been busy to get MIA to compile on FreeBSD, mostly because this seems to be the closest one can get to Mac OS X, and for the latter a MIA user requested help. The git HEAD now compiles properly with clang-3.7 and using ... [More] libc++. Most problems arose from a different behaviour in the explicit instaciation of template, but according to this bug report this might change in newer versions of clang. Most of the dependencies to compile MIA are readily availabe from the FreeBSD package repositories, however maxflow, vistaio, and IT++ need to be compiled and installed manually. It also seems that xsltproc is not available, and hence the user documentation can not be created. There are a few problems though: On one hand the math/blas library is not installed in a usable way, so the shared library /lib/libgcc_s.so.1 must be deleted manually to ensure that the version pulled in by the math/blas package installation is used. Also note, that IT++ will compile even if the blas library is not correctly found, but the it will miss the funcionality that is used in MIA, namely the FastICA algorithm. This will be indicated by failing tests. On the other hand, nifticlib is only available as a static library and on amd64 it can not be linked into the according IO plug-in . The workaround here is to re-compile nifticlib with the -fPIC compile flag. Hopefully, this will be added to the package in the future. The according change is already in the works. [Less]

Thanks to the integration of github with Travis-CI and Coveralls, it has now become possible to get a up-to-date information about the amount the unit tests cover the library code base. Currently, my work on mia focuses on crancking up this coverage by adding more tests.