Dear Audrey,
We experienced the same problem and came up with the following
"processing-pipeline":
1. Coregister T1 onto first functional image
2. Realign and reslice fMRI, then do first level stats
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")
5. Take the individual mask.img (that was created by the 1st level stats)
from all volunteers and also deform them into MNI (using "normalise to
MNI") BUT without smoothing
6. Take all spatially normalised individual mask.img and do a logical AND
with all of them (using imcalc) and use the resulting image as an explicit
mask for the final 2nd level stats.
John Ashburner pointed out that doing an initial segmentation of the T1
images followed by automatic skull-stripping and coregistring the EPIs to
the skull-stripped T1 might get even better results. Importantly, in this
case you need to coregister EPI --> T1 (opposite to point 1 above)
I hope this helps,
-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
[log in to unmask]
http://www.uke.uni-hamburg.de/institute/systemische-neurowissenschaften/
--------------------------------------------------------------------------------
Von: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] Im
Auftrag von Audrey Duarte
Gesendet: Samstag, 1. August 2009 19:41
An: [log in to unmask]
Betreff: [SPM] DARTEL normalisation of partial coverage EPI
Hello there, I was wondering if anyone has tried using DARTEL to normalise
fMRI EPI scans to MNI space with only partial brain coverage? The
resulting images don't look great, with stretching of the images in bits
where there was no coverage. I'm using SPM8 and was applying the flow
fields to realigned and resliced EPIs. The individual structurals were
first coregistered to the EPIs before DARTEL segmentation. Many thanks, Audrey
--
Audrey Duarte, PhD
Assistant Professor
School of Psychology
Georgia Institute of Technology
654 Cherry Street
Atlanta, GA 30332
voice 404-894-2349
http://psychology.gatech.edu/duartelab/
--
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