Dear Jonathan and Marko,
The problem seems to stem from the combined warping and smoothing that is
performed. It always occurs when your EPIs are truncated. Doing some control
analyses revealed that inside the original EPI everything is correct. It's
just that the deformation field enlarge the voxels outside the FOV.
We have designed a pipeline that takes care of these problems (and at the
same time saves a lot of disk space as only the con images are normalized
and smoothed...).
1. Coregister T1 onto first functional image
2. Realign and reslice fMRI, then do first level stats (unsmoothed images!)
3. Use all T1 images --> new segment --> Dartel
4. Take individual con images from first level analyses and apply
deformations (and smooth) them into MNI space (using "normalise to MNI").
These images will again look funny.
5. Take the individual mask.img (that was created by the 1st level stats)
and also deform this into MNI (using Dartel) BUT without smoothing.
6. Take all spatially normalised individual mask.img and do a logical AND
(using IMCALC) with all of them and use the ensuing image as a mask for the
final 2nd level stats.
I hope this works for you
-Christian
--
Prof. Dr. Christian Büchel
Institut für Systemische Neurowissenschaften
Haus W34, Universitätsklinikum Hamburg-Eppendorf
Martinistr. 52, D-20246 Hamburg, Germany
Tel.: +49-40-7410-54726
Fax.: +49-40-7410-59955
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http://www.uke.uni-hamburg.de/institute/systemische-neurowissenschaften/
> -----Ursprüngliche Nachricht-----
> Von: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]] Im Auftrag von Jonathan Peelle
> Gesendet: Dienstag, 1. September 2009 14:57
> An: [log in to unmask]
> Betreff: [SPM] SPM8: DARTEL normalise to MNI problem with
> partial coverage EPIs
>
> I've come across a curious normalization issue using the
> "normalise to MNI" option in SPM8 (with recent updates) on
> partial-coverage EPI scans. Segmentation, coregistration,
> and template creation seem to work ok (see struct_c1_exampfun.png).
>
> Applying the flow field to the segmented structural image
> seems to be fine. However, when I apply the flow field to
> the functional data, I get the strange warping attached (see
> avg152_mwc1_swf.png). This came up at least once previously
> on the list, but I didn't see any replies:
>
> https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0908&L=SPM&P=R
> 399&X=485D484296C56BEE64
>
> Have others run into this issue? Any idea what this might be
> due to, and (even better) possible suggestions for ways to
> fix? Thanks!
>
> Jonathan
>
> --
> Jonathan Peelle, PhD
> MRC Cognition and Brain Sciences Unit
> 15 Chaucer Road
> Cambridge CB2 7EF
> UK
>
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