[MINC-users] classify: bg and csf

[Pedro]

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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>> 
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> _______________________________________________
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