Hi Yune
> It is kind of puzzling that SPM some times generates motion parameters per
> individual runs (e.g., rp_bold1_0000.txt, rp_bold2_0000.txt, etc..) while
> most of time, it generates one file in which the parameters of all the runs
> are included.
> Can anybody explain why this could happen?
The probable answer is:
When selecting the images for realignment, you would typically add
them by session (session = individual run). In this case SPM should
give you an rp_*.txt file for each session. This is helpful because
you would almost always want to split data by session when
constructing a model and analyzing the data, and having a separate
rp_*.txt file for each session makes it convenient to add the movement
parameters as regressors separately for each session.
Alternately, it would be possible to add all of the functional images
as a single session in realign (even though they were collected in
different sessions). In this case you would get a single rp_*.txt
file for all sessions together, because that's how you entered them
(i.e., as far as SPM knows, you just have a single session). This
shouldn't make a difference for the realignment (i.e. in both cases
all the functional images would be aligned with each other), but would
make it somewhat harder to add movement parameters on a
session-by-session basis during analysis.
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However, if you're finding that even after entering scans separately
for each session, you are only getting a single rp_*.txt file, that
seems strange indeed. In that case, if you want to investigate
further, it would probably be good to know which version of SPM you're
using (and with what set of updates)...
Hope this helps!
Jonathan
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