Hi Patricia,
> We feel it is not reasonable to enter all 8 runs in the same realign
> with such a big distance. Or is it?
You could try :) As mentioned by John in the past, between-session
motion is handled differently from within-session motion, in that the
algorithm will try to get all first (or mean) images from all sessions
into one space in a first go. So it may actually work.
> We tried to move the Time2 time series using the "reorient image" option
> in checkreg, so they would be in rough alignment with the time series at
> Time1 before the realign, but found out that as long as the images are
> not resliced, the realign ignores those changes.
It should not. Have you actually applied the changes to all images?
Also, you could try "standard realignment" for all sessions from each
session and then coregistration of the first/mean image of the first
session from Time2 to the first/mean image of the first session from
Time1, *taking along all images* from all sessions from Time2. You can
also use the anatomical images if you have one from each timepoint, as
they will provide better details and may be less vulnerable to different
dropouts etc.
> Is it ok to reslice the
> images twice, once before and once after the realign? (we would like to
> use dartel to register to the MNI space). Or is there a better solution
> to our problem?
Try the above. John has gone to great lengths to avoid instances where
the data needs to be resliced; that alone tells us it is not a good idea :)
Cheers,
Marko
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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