[pymvpa] Preprocessing in FSL, question on specifics

[Mike E. Klein]

Hi all,

I've used FSL/FEAT before, though never specifically for preprocessing for
PyMVPA, so please forgive the simplicity of these questions. I have an
experimental design with several short sessions, so for a standard FSL
analysis (i.e. univariate) I've performed motion correction (etc.) and stats
on each session separately, before running a second level analysis on the
FEAT results. (I should also note that our scanner will output a separate 4D
nifti file for each short session.)

So essentially I'm wondering the best order of events: (a) when to
concatenate the shorter 4D files into one large 4D file, (b) whether I
should run motion correction 1 time (after the concatenation) or whether it
should be run separately for each session's nifti file, before being run a
second time on the concatenated file. While there is very little head motion
within each session, there looks to be considerably more between sessions,
which probably comes as no surprise. A test of running motion correction a
single time (after concatenation) looks like it does not perform very well:
there is still a large amount of motion visible to the naked eye.

As an aside, if I plan to discard some specific volumes, I also would value
any input as to whether it makes more sense to delete them from the 4D time
series (using fslsplit and fslmerge), or to leave them in and give them
their own label ("discard") in the attributes.txt file.

Best and many thanks,
Mike
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