[MINC-users] Classify

[Jon Erik Ween]

Dear list

Sorry about the pics. They can be found at:   http://www.klaru-baycrest.on.ca/index.php?section=969

I figured out that the mask option in classify specifies which voxels  
you WANT to classify (for us in the lesion world, we generally think  
of a mask for those things you DON'T want to include, ie: The stuff  
that will mess up the algorithm). So, the 3DT1 volume I want to  
classify (with lesion mask overlaid and in tal space) is given in  
Picture1. (You'll notice that the registration is not great, I get  
some of the lesion in the ventricle! Any hints as to how to optimize  
the registration with mritotal would be appreciated!).

Running  classify -clobber -user_mask_value 0 -tagfile tags.tag -mask  
14017_083005_combo_lbl2_tal.mnc 14017_083005_3dvol_tal.mnc  
14017_083005_3dvol_cls.mnc

gives me the result you see in Picture2. Lesioned whitematter is  
classified as grey matter and grey matter seems to be way over  
represented.

So, I figured out one way to go around this: Subtract the lesion mask  
from the volume BEORE running classify. The result of this is in  
Picture3. Here, we don't have the problem with lesion being classified  
as grey matter, but normal grey still seems over represented.

Questions:

1) How to optimize the classification so the grey matter is more  
representative of that seen visually on the 3DT1 (particularly the  
cortical ribbon)?

2) When setting tag points in your tag file to feed classify, setting  
paint label value in "Display" to "0" (for background) you don't seem  
to record anything. One work-around I did was to set the value to "4"  
and then edit the tagfile back to "0". Is this normal behavior or am I  
doing something wrong?

3) Saving the tagfile in "Display" gives you a bit different format  
(which classify doesn't like)  compared to the tagfile in ../mni/share/ 
classify/ntags_1000_bg.tag

Display "save labels .tag":  -82 -109 108 1 1 1
/mni/share/classify/ntags_1000_bg.tag:  -82 -109 108 "1"

Am I using the wrong function here?

4) Once I get a classified volume (and I have flair lesion and 3DT1  
lesion in separate masks) how do I calculate volumes? I can't seem to  
find the functions that do this, though suspect they are in minmath or  
minccalc somewhere.

Thanks for all the help!

Cheers


Jon

Soli Deo Gloria

Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
     University of Toronto Faculty of Medicine

Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada

Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca


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On 1-Apr-09, at 7:45 AM, Andrew Janke wrote:

> 2009/3/31 Jon Erik Ween <jween at klaru-baycrest.on.ca>:
>> May I trouble the list with another question? (Guess I'll do so
>> anyhow...)
>
> Hi Jon,
>
> No images... (the list wont accept them)  Can you put them up
> somewhere on the web instead?
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
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>