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

[Andrew Janke]

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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