[MINC-development] label volumes

[Alex Zijdenbos]

Hello all,

Claude and I have been looking at a problem relating to the handling
of label volumes (e.g., atlases) in minc (1.x). There exist a number
of atlas files associated with ANIMAL which have intensity scaling in
them (real range != voxel range). This  causes the labels to appear as
floating point values, which can sometime be several decimal points
away from the integer label value; this in turn can cause label values
to switch over to the adjacent label when manipulated by certain minc
tools.

There are two issues or questions:

1. How *should* label volumes be constructed?

     The simple answer I believe is to make sure that the intensity
mapping is the identity mapping, so that in effect the real values are
equal to the voxel values.

2. How do existing minc tools handle label volumes?

    It turns out that tools like mincmath and minccalc do not have a
-keep_real_range option, and will *always* create slice-specific
intensity mappings. This wreaks havoc on label files. A simple
solution may be to add a -keep_real_range option to tools like
mincmath and minccalc.

Now this is all referring to minc1 - at this point I don't have a
clear view on how this was dealt with in minc2. But either way, i
think mincmath and minccalc should be fixed such as to allow the user
to not destroy minc1 label volumes :)

Thoughts, comments?

-- Alex