[MINC-users] newbee segmentation question

[Soren Christensen]

Hi Jon,
 Just as a first quick check did you see if the transform you got from
register is inverted realtive to what you think it is (ie. definition of
target and source volume). You could add in -invert_xfm in step 4 for a
quick check.

Cheers
Soren

On Tue, May 13, 2008 at 10:27 PM, Jon Erik Ween <jween at klaru-baycrest.on.ca>
wrote:

> 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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