[MINC-users] itk_resample vs mincresample

[Louis Dieumegarde]

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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>End of MINC-users Digest, Vol 126, Issue 11
>*******************************************