Hi, hopefully someone can help.
I have a very basic question that is specific to spm5. I am a little
confused by the documentation and options.
I would like to do a two pass realignment on my fMRI data e.g. 1) create a
mean 2) realign all images to that mean.
In earlier versions of SPM as I understand, two separate realignments had
to be performed to accomplish this. In spm5 does the interface combine
realignments (mean image creation and realignment to that mean image) to
make this possible by selecting images only once?
If this is the case. Do the operations described below do what I want?
In the user interface options for realignment I have chosen "estimate and
reslice"
There is an option under "number of passes". The default option
is "register to mean".
Later in the interface there is the option (as default) to reslice "all
images + mean image"
If I simply input my images keeping all the defaults (which means these
options stay as I have described them) and run the model is it:
1) Going to do the 2 pass procedure I would like, by first creating a mean
and then realigning to that mean?
2) Do something else?
If I need to actually do 2 separate realignments, do I
1) initially coregister and reslice a mean image only (selecting this
option and changing number of passes to "register to first"). It seems
register to mean would be redundant if no mean image existed at this
stage.
2) input my images again and select register to the mean as a second pass?
Thanks in advance.
Cheers
Will
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