Hi Alexis,
> I have a hard time finding a script that does "realign & unwarp" on multiple
> sessions in SPM5, based on the VDM files provided by the Fieldmap toolbox.
> Can anyone help me ?
You need select your files and then call two fieldmap functions in
succession, as in
for i = 2:size(files,1)
s = spm_uw_estimate(files(i,:),opts_unwarp);
spm_uw_apply(s);
end;
You can do that for multiple sessions, bearing in mind that you should
either have one VDM for each session or that you need to make sure the
sessions are in register with each other before using one VDM file. You
also need to set the options (opts_unwarp) according to the requirements
in spm_uw_estimate. It seems advisable to set
% .M - When performing multi-session realignment and Unwarp we
% want to realign everything to the space of the first
% image in the first time-series. M defines the space of
% that.
and
% .sfP - Static field supplied by the user.
> Also it looks like this toolbox is not compatible with 4D nifti files, as when fed
> with such a file, it returns a 3D u-prefixed output file (instead of 4D). Can
> anyone confirm this ?
I think you're right and remember some discussions about that, but I
don't know for sure.
Hope this helps,
Marko
--
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Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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