[MINC-users] newbee segmentation question

[D. Louis Collins]

Jon,

how did you do the registration with register.  The register program  
computes the transform from volume 2 (the middle column) to volume 1  
(the first column).

If you loaded the subject's dataset into column one, and the target  
brain in volume 2, ie:
	register subject_mri.mnc target mri.mnc
then your transform saved is backwards from what you want.

If this is the problem, then the following should solve it:
	mincresample -like standardbrain.mnc -invert_transformation - 
transform target.xfm    lbl.mnc    lbl_stnd.mnc

-Louis

On May 13, 2008, at 4:27 PM, Jon Erik Ween 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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