[MINC-users] Once again: how to use insect properly?

[Andrew Janke]

Myself I always run classify with -clean_tags


a

On 4/19/06, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> The easy change is to edit the script, replacing this line
>
> Spawn(['classify_clean', $TAL, $CLA]);
>
> with
>
> Spawn(['classify_clean', '-clean_tags', $TAL, $CLA]);
>
> I would recommend using tag cleaning in your classification. The default
> behaviour has been changed multiple times as we argue amongst ourselves
> what the default should be. I vote tag cleaning by default. Anyone else?
> Alex?
>
> Jason
>
>
> Ed Gronenschild wrote:
>
> >Hi Jason,
> >
> >I have done like you proposed and got a correct classification,
> >or better, CSF was labeled differently from the background.
> >However, I noticed that the classification in general was different
> >from that without the option -clean_tags. So two questions remain:
> >1. which option should I use?
> >2. how to implement the option -clean_tags in the insect Perl
> >       script? Should I do this myself or do you have a proposal?
> >
> >Cheers,
> >
> >Ed
> >
> >On 14 Apr 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote:
> >
> >
> >
> >>Message: 1
> >>Date: Thu, 13 Apr 2006 12:40:16 -0400
> >>From: Jason Lerch <jason at bic.mni.mcgill.ca>
> >>Subject: Re: [MINC-users] Once again: how to use insect properly?
> >>To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >>Message-ID: <443E7EF0.8080208 at bic.mni.mcgill.ca>
> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >>Ed Gronenschild wrote:
> >>
> >>
> >>
> >>>Hi,
> >>>
> >>>I posted this a week ago and until now I didn't get an answer.
> >>>So once more:
> >>>
> >>>I've used insect to do the classification into WM, GM and CSF. I
> >>>noticed, however,
> >>>that the background gets the same class label (=1) as CSF, so I'm not
> >>>able
> >>>to distinguish CSF from the background. (WM gets label 3 and GM label
> >>>2).
> >>>
> >>>The command was insect input_volume.mnc, where the volume was a T1
> >>>coronal stack.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>Can you try using classify_clean -clean_tags on its own on a file in
> >>stereotaxic space? And, should that not work, can you provide a
> >>listing
> >>of your (prefix)/share/classify directory, where prefix is the package
> >>installation location?
> >>
> >>Cheers,
> >>
> >>Jason
> >>
> >>
> >>
> >>>Have I done something wrong?
> >>>
> >>>The version of insect is from the classify-1.0 package and I' m on a
> >>>Mac OSX 10.3.9.
> >>>
> >>>Ed
> >>>
> >>>
> >
> >_______________________________________________
> >MINC-users at bic.mni.mcgill.ca
> >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


--
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canada->Montreal                                   Cell: +1 (514) 924 2012