[MINC-users] classify: bg and csf

[Pedro]

Transformed tags seem fine. I will send you the files.
Thanks
Pedro

> Em 10 de out de 2016, à(s) 11:18, Alex Zijdenbos <zijdenbos at gmail.com> escreveu:
> 
> Hi Pedro,
> 
> Hrm - you are right - so that is a bug in the documentation:
> 'classify_clean -help' clearly states "non-linear transformation to map the
> tags from stereotaxic space to subject", which is wrong in a few ways (the
> xfm is in fact inverted, and it doesn't need to be a non-linear
> transformation either).
> 
> I would suggest you double-check (using the log file and -tmpdir and
> -keeptmp) whether the tags that are provided to classify itself, are still
> good (contain all classes, and actually match the image). If that doesn't
> clarify it, send the mnc and xfm files and I can take a look.
> 
> -- A
> 
> On Mon, Oct 10, 2016 at 9:57 AM, Pedro <ptcougopinto at gmail.com> wrote:
> 
>> I had understood that the .xfm file was from native to ICBM. I think this
>> transformation is inverted before transforming the tags. Quoting a prior
>> email thread:
>> 
>> <image-to-tags.xfm> is a tranform from your native data space
>> (input.mnc) to the space of the tags. If you are using the ones in the
>> standard package this will be a transform from native space to the
>> icbm152 model.
>> 
>>> Em 10 de out de 2016, à(s) 10:45, Alex Zijdenbos <zijdenbos at gmail.com>
>> escreveu:
>>> 
>>> Hi Pedro,
>>> 
>>> Is it possible that your transform is mapping the tags into oblivion? The
>>> standard set of tags are in ICBM stx space, and the argument to
>>> -tag_transform should be an xfm that maps those standard tags to the
>>> subject image. Just from the file name of the xfm you are using, I'd say
>>> you may need to invert it first?
>>> 
>>> -- A
>>> 
>>> On Mon, Oct 10, 2016 at 9:06 AM, Pedro <ptcougopinto at gmail.com> wrote:
>>> 
>>>> Hi Alex
>>>> 
>>>> $ classify_clean -tag_transform t1_2talnlin.xfm -mask mask.mnc
>>>> -mask_source t1.mnc t1_class.mnc
>>>> 
>>>> Shouldn’t classify_clean be using background tags from
>>>> /opt/minc/share/classify/ntags_1000_bg.tag by default?
>>>> 
>>>> 
>>>>> Em 7 de out de 2016, à(s) 22:27, Alex Zijdenbos <zijdenbos at gmail.com>
>>>> escreveu:
>>>>> 
>>>>> Hi Pedro,
>>>>> 
>>>>> My guess would be that you are not providing classify with (a)
>> sample(s)
>>>> of 'bg'. Exactly how are you invoking it?
>>>>> 
>>>>> -- A
>>>>> 
>>>>> 
>>>>> Sent from mobile
>>>>> 
>>>>>> On Oct 7, 2016, at 12:51, Pedro <ptcougopinto at gmail.com> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I´m getting background and CSF to have the same label value with
>>>> classify. Is it possible to avoid this? I tried using -mask -mask_source
>>>> brain_mask.mnc, still with background labels as ‘1’.
>>>>>> 
>>>>>> Thanks
>>>>>> Pedro
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>>>>> _______________________________________________
>>>>> 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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>> 
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