From vladimir.fonov at gmail.com  Thu Mar  3 18:10:33 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 3 Mar 2016 18:10:33 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
Message-ID: <56D8C469.2090109@gmail.com>

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

From a.janke at gmail.com  Thu Mar  3 19:45:14 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 4 Mar 2016 10:45:14 +1000
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <56D8C469.2090109@gmail.com>
References: <56D8C469.2090109@gmail.com>
Message-ID: <CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>

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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From mishkind at gmail.com  Thu Mar  3 21:40:40 2016
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Thu, 3 Mar 2016 16:40:40 -1000
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
References: <56D8C469.2090109@gmail.com>
	<CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
Message-ID: <CAB-GmL0dxzxyY=GJECRTy-4+FrMz=R2=XEHNyJ=X6t7O+0H2Hw@mail.gmail.com>

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
>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>

From robert.d.vincent at mcgill.ca  Fri Mar  4 07:03:13 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Fri, 4 Mar 2016 07:03:13 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
References: <56D8C469.2090109@gmail.com>
	<CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
Message-ID: <CAAd5DeRDuYKhV+uMKMCxMWQS85hd0t=28nRtCRAcratZCiokaw@mail.gmail.com>

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
>>
>
> _______________________________________________
> 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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From zijdenbos at gmail.com  Fri Mar  4 08:19:38 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 4 Mar 2016 08:19:38 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <CAAd5DeRDuYKhV+uMKMCxMWQS85hd0t=28nRtCRAcratZCiokaw@mail.gmail.com>
References: <56D8C469.2090109@gmail.com>
	<CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
	<CAAd5DeRDuYKhV+uMKMCxMWQS85hd0t=28nRtCRAcratZCiokaw@mail.gmail.com>
Message-ID: <1DA5B6C0-DE04-48AB-AA85-6078DA5ED2A3@gmail.com>

Very cool - I didn't think this was ever going to be tackled :))
Great work!

-- A


Sent from mobile

> On Mar 4, 2016, at 07:03, 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
>> 
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> 
> _______________________________________________
> 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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From vladimir.fonov at gmail.com  Fri Mar  4 10:14:06 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 4 Mar 2016 10:14:06 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <CAAd5DeRDuYKhV+uMKMCxMWQS85hd0t=28nRtCRAcratZCiokaw@mail.gmail.com>
References: <56D8C469.2090109@gmail.com>
	<CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
	<CAAd5DeRDuYKhV+uMKMCxMWQS85hd0t=28nRtCRAcratZCiokaw@mail.gmail.com>
Message-ID: <CAMCwi7OeUxk0c4sonJ9CjqQPmroBOZg=gdkSFVpjnqkVYc+QiQ@mail.gmail.com>

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
>>>
>>
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>
>>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
>


-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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From v.s.fonov at ilmarin.info  Fri Mar  4 09:57:44 2016
From: v.s.fonov at ilmarin.info (Vladimir S. FONOV)
Date: Fri, 4 Mar 2016 09:57:44 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <CAB-GmL0dxzxyY=GJECRTy-4+FrMz=R2=XEHNyJ=X6t7O+0H2Hw@mail.gmail.com>
References: <56D8C469.2090109@gmail.com>
	<CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
	<CAB-GmL0dxzxyY=GJECRTy-4+FrMz=R2=XEHNyJ=X6t7O+0H2Hw@mail.gmail.com>
Message-ID: <35D4784A-3EDB-4E2E-8926-F1A751860B93@ilmarin.info>

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
>> 
>> 
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>> 
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development

Best regards, Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info





From vladimir.fonov at gmail.com  Fri Mar  4 10:30:20 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 4 Mar 2016 10:30:20 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <CAB-GmL0dxzxyY=GJECRTy-4+FrMz=R2=XEHNyJ=X6t7O+0H2Hw@mail.gmail.com>
References: <56D8C469.2090109@gmail.com>
	<CAG0CB20OWNsnXbt6ah7rCoZ4u+WPUu9PFhS-n_W23njAV5u5zg@mail.gmail.com>
	<CAB-GmL0dxzxyY=GJECRTy-4+FrMz=R2=XEHNyJ=X6t7O+0H2Hw@mail.gmail.com>
Message-ID: <CAMCwi7O_CK9bYi0RBtDs3bHde2F7GEoVj_+1o=_QbZqoXni7+g@mail.gmail.com>

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
> >
> >
> > _______________________________________________
> > MINC-development mailing list
> > MINC-development at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> >
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
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From peter.neelin at gmail.com  Sat Mar  5 09:56:24 2016
From: peter.neelin at gmail.com (Peter Neelin)
Date: Sat, 5 Mar 2016 09:56:24 -0500
Subject: [MINC-development] -labels support in minccalc,
	mincmath and mincresample
In-Reply-To: <56D8C469.2090109@gmail.com>
References: <56D8C469.2090109@gmail.com>
Message-ID: <CANcjydY6N0rA_zx8gGudgkPCRGu9pXBkgBVS-sf+MoR9dBGbcw@mail.gmail.com>

Hallelujah!!

15 or 20 years after the need was identified. There must be a collective
sigh of relief from the community! This makes me very happy from a sense of
closure perspective.

Thank you, Vladimir.

Peter
On Mar 3, 2016 18:10, "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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