Hello,
just a short reply to your second question:
> Furthermore I know that people tend to discard "the first few scans" to
> allow for saturation effects. Am I correct in assuming that this means
> the first few scans of each run (of about 10-12 minutes)? And does it
> make a difference whether the discarding is done before or after
> preprocessing?
Yes, and yes :) The idea of discarding a few scans at the begin of each
run is that you want to avoid T1 effects, as the first scan will have a
slightly different contrast than the second one, and the third one, and
... most people will not go much further, but it depends too much on
your sequence and scanner and field and ... to give a general rule as in
"throwing out 4 will always be enough". However, it does make a
difference for processing as, for example, realignment will, at some
point, take the first image as a reference, and if this is very
different in contrast from the others it will not be a good reference.
Similar problems may occur at other steps, so I would suggest throwing
your first images away before doing anything to the data.
Best,
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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