Hi Alle Meije,
the easiest way to combine both realign and coregistration would be to
create a batch containing file selector(s) and all processing steps,
linked with dependencies. This batch would then describe a work flow per
subject. The subject specific items (directories in this case) would be
left empty.
The batch GUI "Save batch and Script" option will then save a batch and
a MATLAB script skeleton that will help you to fill in all directories
for all subjects and finally run all jobs.
If your subject directories are stored in a cellstr variable subjdirs,
then you could easily derive T1 or fMRI session directories like this:
subjdirs = {
'/data/subject1'
'/data/subject2'
};
T1dirs = cellfun(@(cdir)fullfile(cdir,'T1'),subjdirs,'UniformOutput',false);
encdirs =
cellfun(@(cdir)fullfile(cdir,'enc'),subjdirs,'UniformOutput',false);
You would need to enter these directories separately, but the script
template will help you do this efficiently. The batch file selector does
not (yet) allow to filter full path patterns.
Volkmar
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