One way to do it is, as you suggest, just put all the runs into the same
bold directory, then just use mc as registration. This works to some
extent. The main problem with it is that you can get fairly different B0
distortion between sessions because of the different head/body position
in the scanner, and this can cause the mc algorithm to moderately
misalign the sessions. You can try it out and see how well it works
using tkregister2 (can't fixed it with tkregister2 though).
The other thing you can do is to analyze each session separately, then
combine them together in talairach space with a fixed effects analysis
(isxavg-fe-sess), assuming you've done the first couple of freesurfer
analysis steps.
>> is it necessary/helpful to record low-res anatomicals before
functional runs
I don't find it helpful for registration purposes, though you do need
good anatomicals at some point.
doug
Sebastian Moeller wrote:
Dear fs-fast wizards,
doing monkey fMRI in Bremen (block desing so far) I run into the
problem that analysing the data from one session does not lead to well
defined activation maps. Therefore I would like to pool over several
sessions (always within one subject). Unfortunately I have did not
manage to always position the slices at the same position, I recorded
a different number of runs each session. Now my assumption is all I
need to do is define according df and sf files and be done with. But
at what stage (mc-sess, spatialsmooth-sess, mkanalysis-sess.new,
selxavg-sess, mkcontrast-sess or stxgrinfer-sess)? Is it advisable to
motion correct all session runs together, or combine the data after
that step? So excuse me for my uneducated question, but I would be
delighted to tap into this list's vast knowledge before debarking into
computationally long experiments.
One more question, is it necessary/helpful to record low-res
anatomicals before functional runs to register separate sessions, or
is this step avoidable.
Regards
Sebastian
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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