Hello,
I am new to fMRI analysis and using FSL, so excuse me if there is something
obvious I am overlooking in the following query.
I am busy preprocessing fMRI data from a Go/NoGo task. Each person gets
scanned twice (once on placebo, once on medication), with 12 runs of the
task in each scan. I have noticed that the functional data is inverted with
respect to the standard space and T1 structural image after registration for
some of the runs (but not for others).
It was suggested to me on inspection of these images that this inversion
might be occuring due to the parameters for brain extraction of the fMRI
data being too lenient, with the result that there is a lot of noise outside
of the brain which is throwing the registration algorithm off. Indeed, if I
use the BET GUI to process the fMRI data, and then use the resulting brain
image as input to the preprocessing step in FEAT (with the BET brain
extraction option under the Pre-stats tab disabled), the problem with
registration disappears (please see the images at
http://projects.pry.uct.ac.za/uploads/fMRI for examples).
My first question is whether running BET on the fMRI data prior to
processing motion correction using FEAT is a legitimate procedure? It has
been mentioned in another post to this list that running BET prior to the
other steps might confuse mcflirt, due to the creation of "artificial
intensity boundaries" (message: 017723). However, this does seem to solve
the registration problem, and the differences in the average displacement
picked up by mcflirt are slight when doing it this way and enabling bet in
FEAT (though see below).
I have subsequently noticed that enabling the BET function in FEAT does not
actually appear to make any difference to the registration (as seen from the
images produced). This is confirmed by the identical results produced when
switching this option of and off, and the fact that no difference is
observed when changing the -f parameter from 0.3 to 0.5 in featlib.tcl. My
second question therefore is why this should be the case (it is a whole
brain analysis so there are no FOV issues that would switch bet off)? Is
there some way of forcing bet to run in FEAT?
Regards,
Jonathan Ipser
Department of Psychiatry and Mental Health
University of Cape Town
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