[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 Mar 3, 2016, at 21:40, 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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Best regards, Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info