[MINC-users] The future of MINC

[Vladimir S. FONOV]

Hello Everybody,

looks like I missed this somehow.
Pierre Bellec wrote:
> @ Andrew
>> I had the feeling that EZminc was developped to cope with some
>> shortcomings of the existing
>>> libraries.
>> EZminc to my understanding was a bit of glue between the C MINC
>> interface and ITK for vlads needs. Sort of akin to what volume_io was
>> originally for Dave McDonald. Still I don't think the C MINC2
>> interface needs changing, it works and works well. Pity none of the
>> minc tools use it yet but that's another issue....   I think dumbing
>> down the C MINC2 interface would be a bad idea, very few people use
>> all the features of MINC (eg: block structured files, MINC ID's,
>> automatic History, world + voxel co-ordinates, Big vs Little endian
>> resistance) and most of the glue (R/Matlab/Octave/python) libraries
>> from what I have seen take a very simplistic approach to reading a
>> file. That is: gimmie the file, gimmie all of it, I'll put it in a big
>> short/float array called minc.img. This approach is fine and serves a
>> purpose (and usually well). The point is
>> mincmath/mincaverage/mincresample/minccalc/mincstats _can_ be used on
>> multiple MINC files that are over 10GB in size and yet only use a
>> small amount of memory/CPU.

1. ezminc allows to open a minc file and read/write it slice-by-slice. 
So, I have programs dealing with 100s of files simultaneously, with 
total amount of data exceeding total memory several times. This part 
does not translate to ITK ,though.

2. I don't know how easy volume_io really is. Everybody whom I know who 
used it at some point, basically hit a stone wall trying to solve 
intensity normalization problem. Slice normalization and ICV is still a 
bit of a black magick for me, especially when I am dealing with discrete 
values.

3. Right now there are two independent APIs - one legacy which allows 
one to access minc1 and minc2 files and a new one, which only works with 
minc2. I gave up on newer api after I learned (several years ago) that 
there are still unsolved problems, again related to intensity 
normalization.

-- 
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info