[MINC-users] newbee segmentation question

[Jon Erik Ween]

Hi

First time on list, sorry if I've missed similar threads before, but  
nothing popped up with any search. I'm hoping someone has a hint!

Issue: I'm trying to get stroke lesion segmentations  into standard  
space to finally plug into VLSM (Bates et al) to correlate with  
behavioral measures. Problem is, I have non-standardized (clinical)  
scans to work with. Here's my procedure:

1) Convert DICOMs into mnc format using UCLA debabeler. Seems to work.
2) Generate a transform (target.xfm) from target scan to standard  
scan using Register. Looks good enough.
3) Segment lesion in target brain using threshold fill in Display and  
"save labels as mnc" (lbl.mnc). Looks good.
4) Resample labels into standard space using:
mincresample -like standardbrain.mnc -transform target.xfm    
lbl.mnc    lbl_stnd.mnc
Reloading the transformed lbl_stnd.mnc on top of standardbrain.mnc in  
Display and the segmentation is WAY off, not even close.

Would anyone know what I'm doing wrong?

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

Kimmel 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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