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[12/12/2005] Ph.D. Studentship: Assessing the Effectiveness of Non-Rigid Registration in the Measurement of Cortical Thickness

Distinctive patterns of accelerated cerebral atrophy are a feature of a large number of neurodegenerative and dementing disorders such as Alzheimer's disease, frontotemporal dementia, Parkinson's disease and others. Regional measurements of cortical thickness from MR images can therefore provide information on the progression of these diseases. However, in order to compare such measurements across groups of patients, the image volumes must first be aligned into a standard coordinate system. This process is known as registration.

The goal of this project is to evaluate the improvements in the accuracy of cortical thickness measurements gained through using more complex registration algorithms. A comparison will be performed between rigid registration, which aligns the images only through translation, rotation, and scaling, and non-rigid registration, which attempts to align the image volumes at every point. Cortical thickness measurements will be computed using both approaches, and any improvements gained through the use of non-rigid registration will be quantified.

Applicants should have, or be about to obtain, a degree in a numerate science, and have an interest in statistics and numerical programming techniques. Experience of programming would be an advantage.

Details of the current round of strategic studentships at the University of Manchester School of Medicine can be found here, and details of the application procedure can be found here.

[5/4/2006] This vacancy is no longer available.

[19/09/2005] A tinaTool that allows the loading of astronomical images from the FITS (Flexible Image Transport System) file format has been added to the TINA projects directory of the CVS repository. Memo no. 2005-014 contains full instructions on how to obtain, install, and use the new tool.
[01/08/2005] Computer Vision: Machine Learning of 3D Projected Shape.

A student is required for a collaborative project to develop a learning system for the recognition of 3D projected shape.

The approach is based upon extension of published work and software. This includes neural network architectures and statistical methods for data representation and analysis which are thought to closely replicate aspects of processing in the human brain. Details of recent work can be found at our open source web site www.tina-vision.net. No prior knowledge of the statistical mechanisms underlying brain function are expect, as this will be provided as part of research training. However, this area of work is a challenging topic which will require a good numerical first degree and an interest in algorithmic research programming.

The project will involve a close collaboration with the research team at Siemens Corporate Research in Princeton U.S.A. and will therefore require regular overseas visits. The project is to be funded under the government funded Faraday partnership scheme, which provides an increased student stipend and is well provisioned for additional resources and travel. Prospective applicants should contact Dr Neil Thacker (neil.thacker@man.ac.uk) or Dr Paul Bromiley (paul.bromiley@man.ac.uk) for further details.

[12/12/2005] This post has now been filled.

[27/06/2005] A colour image input/output/segmentation tool, based on the algorithm described in Tina Memo no. 2001-015, has been added to the Tina libraries. It is available in the example2 toolkit (in tina-tools/toolkits/example2).
[08/03/2005] A live cd distribution, based on KNOPPIX 3.7 and containing the TINA 5 software (together with some other software useful for TINA users, such as DDD, Gnuplot, Xgobi, and Maxima) has been produced and is now available from the TINA KNOPPIX webpage.
[22/02/2005] Packaged versions (tarballs) of the tina-libs and tina-tools are now available from the software page. They are updated nightly, and so should contain the same code as the CVS repository.
[21/02/2005] We are building a page listing classic papers in medical image analysis and machine vision on the wiki page. This allows discussions of various aspects of research in these fields. Hopefully, it will evolve into a valuable teaching resource.
[10/02/2005] After months of delicate negotiations with IT support, the mailing lists should now be working.
[08/02/2005] The teaching pages have been updated with details of the MSc courses for 2005.
[07/01/2005] During the Christmas period a vulnerability in QWikiWiki has been discovered: I have taken down the wiki site on the developers page for the time being to stop anyone hacking the rest of the web site. Hopefully, the wiki site will be restored on Monday. Sorry for the inconvenience. Update 12/01/2005: wiki page is now back online.
[17/12/2004] Added a page for Tina 4, with tarballs of all library versions, tarballs of the Tina 4 projects, and lxr and doxygen code browsers. NOTE: this deprectated software, provided here only for historical interest and for equivalence testing of Tina 5 algorithms.
[16/12/2004] Added a page for teaching materials, with the pre-course material (including MATLAB lab sessions and a quiz) and the practical session handouts for the MSc module taught by the core group programmers. This page also has links to all of the tutorial memos.
[14/12/2004] The online image library from the old Niac web pages is now available under the "images" link.
[13/12/2004] Online versions of the user guide, programmers guide, and programmers reference guide are now available on the software page.
[9/12/2004] The doxygen and lxr code browsers now rebuild automatically at 3am from code freshly checked-out from the CVS repository, so if you commit new code, it will be indexed by the next morning.
[7/12/2004] The FAQ page has been populated with the questions and answers from the old Niac pages, slightly updated for Tina 5.
[3/12/2004] The documents page on the website has been restructured to emphasise the Tina memos. The memos themselves have been distributed across four directories: technical, which includes user and programmer's guides for Tina, together with guides to associated software; statistical, which includes memos on mathematics and statistics; vision, which includes memos on machine vision; and medical, which includes memos on medical image analysis. A complete index of all memos is also available.
[30/11/2004] Major update to the Tina build system. A simple build system, much like the one used by Tina 4, is now available. Read the documentation in the tina5_simple_build.sh script in tina-libs for instructions on how to use it.
[6/8/2004] Major update to the coregistration tool. Mutual Information coregistration is now available in Tina 5.
[4/8/2004] At some point before 7/6/2004 the server holding the Tina 5 CVS repository was hacked and the repository lost, together with the web pages, wiki pages, code browsers etc. We have now set up a new server and are in the process of setting up the services that used to be available on the web pages. Anonymous access to the CVS repository now works.

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