On Dec 6, 2007 3:32 PM, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > I just read the UWeek article about SAGE and am wondering about > how complete the matlab-style functionality is. I'd really like to > ask > some people to try their matlab code on it if possible. The shared > workbooks would also be a big plus. > > I am a Sr Computer Specialist for a research group here at UW. > We make use of matlab but have had problems with licenses > (especially for specialized toolboxes) being used up by > long-running processing. > > We especially do image and signal processing for fMRI, etc. and also > use the brain image analysis package Statistical Parametric Mapping > which is itself open source but requires matlab. I'd love to hear if > anyone is running SPM in SAGE! > http://www.fil.ion.ucl.ac.uk/spm/
SPM can be run from within python by using the mlabwrap bridge code, I think: http://mlabwrap.sourceforge.net/ For fMRI functionality, I'd invite you to look at: http://neuroimaging.scipy.org/ This project (NIH funded) is led from UC Berkeley and it has recently hired two full-time developers, who are currently focusing on the numpy/scipy foundation and will be soon moving much of their effort towards the higher-level layers. Several other members from the Berkeley lab are also participating. In addition, Jonathan Taylor is actively contributing a lot of code he's developed recently, a team from Neurospin also regularly contributes code (Alexis Roche, Bernard Thirion, Philippe Ciuciu, Sebastien Meriaux, etc), and Matthew Brett from Cambridge is actively involved in the whole project. You can see the commit history here: http://projects.scipy.org/neuroimaging/ni/timeline The intent of the nipy project is to develop a complete set of functionality for fmri analysis, with a fully open set of algorithms so that new approaches and ideas can be tried, often beyond the assumptions of SPM. There are several toolkits for scipy (scikits) that are also being developed (machine learning, manifold dimensionality reduction) that will contribute to this effort. The philosophy of this project is to contribute directly to numpy or scipy the functionality that can benefit other non-neuroimaging fields, and to add the neuroimaging-specific functionality in the nipy codebase. We'd be thrilled to have the participation of more devlopers, if you are interested. Needless to say, since this is all python/numpy/scipy based, it can be used from within Sage at any time, it's just one more python package. Cheers, f --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/ -~----------~----~----~----~------~----~------~--~---
