MINC/Future/Tconf20110223

Notes for conference call on the Future of MINC, held Feb 23, 2011 Present Patrick, Jim, Mallar, Marc, Samir (all the way from Singapore), John, Jason, Pierre, Alex, Mishkin, Anka, Dniel, Simon D, Simon E, Vlad & Louis Topics What is the goal of MINC? What is our goal? MINC is a complex, powerful image file format that is self documenting, self describing, extensible, portable and specific for n-dimensional medical images. MINC has a standard API to ensure that files are read/written always conform to the MINC definition. Our goal is to guarantee a future for MINC (and the MINC tools) in the face of competing file formats and software packages by simplifying the installation and use of the MINC libraries and tools. From the users – the main request is simplicity: Simple installation, single point of contact for progs/docs Up-to-date documentation Example software Example analyses A user interface Software Distributions/ Computer systems supported Linux ( Debian, ubuntu, redhat, ) Mac Windows This could open up a large user-base but have issues with effort/resources. related to GUI One package vs many small packages License issues – what can be bundled and what can’t (MINC vs GPL license) Testing Comprehensive testing is required for each release Dashboard-style testing/reporting? I/O Bindings for R (Jason’s RMINC and Jim's newer and better mincIO) Python (Jason’s https://launchpad.net/pyminc) Octave, Matlab( Pierre’s NIAK) C/C++ Vlad’s EZminc, David’s volumeIO CImg supports minc (http://cimg.sourceforge.net/) MINC1 vs MINC2 API support and use ITK & VTK – currently with limited support. NIFTI support? Lots of advantages from user’s perspective at first glance, but… Disadvantages: Viewer-centric definition of data ordering (radiological vs neurological) without this information in the file header lack of robust coordinate system information lack of intensity mapping info will the users rise up and bite us? What to link/association with Neurodebian (Michael Hanke's neuro.debian.net) Integration with other software tools Osirix, ITK-snap, Elastix, ANTs Software development tools Needs: include/integrate external developers (who can submit/ who do we trust?) proper bug tracking (Jim): real, live minc bugs can make sure that the bug has been noted by minc-dev and have some idea WRT fix status. Perhaps such a system could be integrated with a compensation model in which fixes or (approved) feature requests would be assigned a monetary value and then devs would be free to "sign-up" to work on a given request? distributed version control systems yet? (git, hg, bzr, etc.) Possibilities: CVS repository @ MNI (or elsewhere) NITRC (www.nitrc.org, they are keen to have us join + do they have git?). Launchpad (launchpad.net) Google code, track Documentation http://en.wikibooks.org/wiki/MINC/ http://en.wikibooks.org/wiki/MINC/Tutorials FAQ Example code MINC tools not in standard distribution structure segmentation tools Brain extraction mincBET ANIMAL structure segmentation (Collins) Hippocampus + MTL structures fusion labelling (Collins) thalamus + basal ganglia (Mallar) Lateral ventricle segmentation (V.Fonov) surface segmentation CLASP (Evans) Analysis tools fMRI stat NIAK (Pierre B) ITK Snap (Vlad's mods for minc; if minc properly supported in ITK, then this mod not needed) ElastiX (Dante) viewnup (Andrew) PVE (Jossi) Action items: Who wants to participate Who can be in charge of what What is the next step MINC Workshop / course