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

[Vladimir S. FONOV]

There is a special datatype "label" in MINC2 file format, unfortunately it
is not supported by any standard minc tools.
Maybe somebody could modify MINC1 API to properly translate this data type
to an integer class for legacy apps ?
I.e see
https://github.com/BIC-MNI/libminc/blob/master/testdir/minc2-label-test.c

On Fri, Mar 4, 2016 at 7:03 AM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Vlad,
>
> Thanks for tackling this - it's long overdue. Regarding Andrew's comments,
> I'll look into adding support for the long-neglected "class" field we
> defined for MINC 2 files - it was supposed to help solve this problem, by
> marking label files as one of "real", "integer", "label", etc.
>
>    -bert
>
> On Thu, Mar 3, 2016 at 7:45 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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