# 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