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

[Jason Lerch]

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
>  
>