[MINC-development] -labels support in minccalc, mincmath and mincresample

[Vladimir S. FONOV]

Hello,

unfortunately, using -nearest_neighbour does not guarantee absence of the
slice-normalization rounding error. So, one will have to use -labels
-nearest to achieve the desired effect.

On Thu, Mar 3, 2016 at 9:40 PM, Mishkin Derakhshan <mishkind at gmail.com>
wrote:

> really a great idea and very much needed for minccalc and mincmath.
> for mincreseample, would this be any different than using
> -nearest_neighbour?
>
> On Thu, Mar 3, 2016 at 2:45 PM, Andrew Janke <a.janke at gmail.com> wrote:
> > ace stuff.
> >
> > I like it a lot.  any chance we can introduce a label header tag
> somewhere
> > so that this happens by default for label files?
> >
> > I can think of a few edge cases but this should usually be right?
> >
> > thanks
> >
> > a
> >
> > On 04/03/2016 9:10 AM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
> wrote:
> >>
> >> Hello MINC developers,
> >>
> >>
> >> I made changes to libminc (
> >> https://github.com/BIC-MNI/libminc/tree/develop-labels )
> >>
> >> And minc-tools (
> https://github.com/BIC-MNI/minc-tools/tree/develop-labels
> >> ) to add support for -labels option in minccalc,mincmath and
> mincresample,
> >> to try to address the common problem that many people seem to have over
> and
> >> over again and again - inter-slice normalization of volumes with integer
> >> labels.
> >>
> >> Description of the problem:
> >>
> >> When you have a minc file that contains discrete levels (i.e anatomical
> >> labels) produced, for example, by manual labeling in Display or
> ITK-SNAP.
> >> You apply some simple operation using minccalc (for example intersecting
> >> your labels with a mask, or doing some logical operations) you
> inadvertently
> >> produce a volume where the actual discrete values for voxles are
> replaced by
> >> floating-point ones. What's worse is the rule of this replacement
> depends on
> >> the data type used for the minc file, dimension order of the file and
> >> particular location of the voxel within the file.
> >>
> >> Example:
> >>
> >> minccalc  -express 'A[0]*2'
> >>
> /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_deep2.mnc
> >> test.mnc
> >>
> >> Here I take a file that contains 15 labels describing deep gray matter
> >> structures and multiply each label by 2.
> >> The contents of the input file (using print_all_labels):
> >> Label: 1 6931
> >> Label: 2 16801
> >> Label: 3 1499
> >> Label: 4 175210
> >> Label: 5 5789
> >> Label: 6 1404
> >> Label: 7 909
> >> Label: 8 4992
> >> Label: 9 8512
> >> Label: 101 6931
> >> Label: 103 1499
> >> Label: 106 1404
> >> Label: 107 909
> >> Label: 108 4992
> >> Label: 109 8512
> >>
> >> The contents of the output file :
> >> Label: 2 6649
> >> *Label: 3 282*
> >> Label: 4 16801
> >> Label: 6 1499
> >> Label: 8 175210
> >> Label: 10 5789
> >> Label: 12 1404
> >> Label: 14 857
> >> *Label: 15 52*
> >> Label: 16 4992
> >> Label: 18 8512
> >> Label: 202 6931
> >> Label: 206 1499
> >> Label: 212 1404
> >> Label: 214 857
> >> *Label: 215 52*
> >> Label: 216 4992
> >> Label: 218 8512
> >>
> >>
> >> Note the highlighted Labels: 3,15,215 which are clearly not possible
> when
> >> one multiplies integer labels by 2.
> >>
> >> Solution (using the -labels option):
> >> minccalc -labels -express 'A[0]*2'
> >>
> /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_deep2.mnc
> >> test_labels.mnc
> >>
> >> The output is now correct:
> >> Label: 2 6931
> >> Label: 4 16801
> >> Label: 6 1499
> >> Label: 8 175210
> >> Label: 10 5789
> >> Label: 12 1404
> >> Label: 14 909
> >> Label: 16 4992
> >> Label: 18 8512
> >> Label: 202 6931
> >> Label: 206 1499
> >> Label: 212 1404
> >> Label: 214 909
> >> Label: 216 4992
> >> Label: 218 8512
> >>
> >>
> >> --
> >> Best regards,
> >>
> >>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> >> _______________________________________________
> >> MINC-development mailing list
> >> MINC-development at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >
> >
> > _______________________________________________
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> >
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>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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