[MINC-users] itk_resample vs mincresample

[Vladimir S. FONOV]

Hello,


are you sure that your input file doesn't have this problem?
What is the output of
mincheader volume.mnc |grep 'image-min\|image-max'


--normalize switch has nothing to do with interpolation of labels, it 
only affects spacial sampling.

On 16-02-24 10:58 AM, Louis Dieumegarde wrote:
> Bonjour,
>
> We had problems with the labels values being re-evaluate with mincresample when we do a nereast-neighbour.
>
> I’m trying itk_resample as suggested with the —labels option but it seems to do the same.
>
> Is the option —normalize of itk_resample should be consider as it seems to keep the exact value of labels?
> What is the difference between —normalize and —labels options?
>
> Merci.
>
> Louis Dieumegarde, B.Sc.
> Professionnel de recherche
> Laboratoire Medics, local F-3568
> Centre de Recherche de l’Institut Universitaire en Santé Mentale de Québec
> 2601 Chemin de la Canardière, Québec
> G1J 2G3, Canada
> (418) 663-5000, poste 6716
> louis.dieumegarde at crulrg.ulaval.ca
>
>
>
>
>
>
>
>
>
> On 2016-02-21, 12:00 PM, "minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca" <minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca> wrote:
>
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>> Today's Topics:
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>>    1. Re: Problems with volume/slice normalization and labels
>>       (Gabriel A. Devenyi)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sat, 20 Feb 2016 16:36:34 -0500
>> From: "Gabriel A. Devenyi" <gdevenyi at gmail.com>
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Subject: Re: [MINC-users] Problems with volume/slice normalization and
>> 	labels
>> Message-ID:
>> 	<CAFQOoOqiZ0CKL62PzZEskfB-89k7c8z64rDBOhB7ZG_aeOij9A at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Thanks Vlad, we've moved to itk_resample for our transforms previously on
>> your recommendation.
>>
>>
>>
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>>
>> On Tue, Feb 16, 2016 at 1:20 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>>> wrote:
>>
>>> itk_resample --labels <in> <out>  --like <template> --transform
>>> <transform.xfm>  for resampling
>>>
>>> or, after running any standard minc tool (minccalc, mincmath, etc )
>>>
>>> mincreshape -valid_range 0 X -image_range 0 X <in> <out>
>>>
>>> where X in you maximum label id
>>>
>>> On 16-02-16 12:09 PM, Gabriel A. Devenyi wrote:
>>>
>>>> Hi minc-users,
>>>>
>>>> I have some labels that via some step in minc-toolkit had an introduction
>>>> of volume and/or slice-selective normalization.
>>>>
>>>> This is causing serious issues *sometimes* in some processing.
>>>>
>>>> Can anyone recommend a way to successfully strip away all the
>>>> normalization
>>>> from the file so they are true labels?
>>>>
>>>>
>>>
>>> --
>>> Best regards,
>>>
>>>   Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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>>
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>> End of MINC-users Digest, Vol 126, Issue 11
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-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com