[MINC-users] classify_clean

[Paul Rasser]

Thanks Andrew.

re: -tagfile -bgtagfile, in a way yes, as I have tested with -tagdir to point to the custom inverted tags (which I call ntags_1000_bg.tag and ntags_1000_prob_90_nobg.tag) , but  -tag_transform looks like it might be a better option.

Also, any help with the  reference for classify_clean and nlfit_smr would be greatly appreciated.

Thanks again,
Paul


>>> Andrew Janke <a.janke at gmail.com> 04/11/11 4:51 PM >>>
Hi Paul,

On 4 November 2011 14:03, Paul Rasser <Paul.Rasser at newcastle.edu.au> wrote:
> I'm looking to use classify_clean to classify volumes in native space and was hoping for suggestions/concerns with respect to using it in the following way:

I generally always do tissue classification in model space but I can't
see any reason as to why this approach won't work.

> #find nl transformation
> nlfit_smr subj.mnc nl.xfm -model colin27_t1_tal_lin
>
> #invert transformation
> xfminvert nl.xfm  nl_inv.xfm
>
> #invert .tag files to subject's native space
> transform_tags ~/ntags_1000_prob_90_nobg.tag nl_inv.xfm ntags_1000_prob_90_nobg.tag
> transform_tags ~/ntags_1000_bg.tag nl_inv.xfm ntags_1000_bg.tag
>
> #apply classfy_clean to subject in native space
> classify_clean -clean_tags subj.mnc subj_seg.mnc

I take it you also supply -tagfile -bgtagfile arguments so that your
custom tags are used?  Either that or you can always skip transforming
the tags and instead supply a  -tag_transform <nl_transform.xfm>
argument.



a
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