> I have a few very basic questions that are specific to spm5. I am a
> little confused by the documentation and options. I have read the manual
> but still dont understand all the options (as I dont know how to check if
> they have worked). I'm sure I can get by but I would like to understand
> completely. Could someone answer the following questions please?
>
> 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, two separate realignment passes had to be
> performed to accomplish this.
> In SPM5 does the user interface options combine realignments (mean image
> creation and realignment to that mean image) to make this possible by
> selecting the realignment option (and your images) only once??
Yes, but note that the resulting matrices (written to the .hdr files) are
adjusted so that the first image in the series is not moved. The results
should be similar to those that would arise from all images being aligned
with the first - except they are (hopefully) a bit more accurate.
>
> If this is the case, do the operations described below do what I want?
> Initially I select all my raw images (I do not have a mean image).
> 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". This is what I have done, but I wonder if a mean
> image has to be present before it can do this (or if it creates a virtual
> one for the job at hand)??
A mean image is created on-the-fly after the first pass.
> Later in the interface there is the option (as default) to reslice "all
> images + mean image". This is also what I have selected.
>
> If I select exactly what I have described above 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?
It does something else:
i) Realigning images to the first, and creating a mean image on-the-fly.
ii) Realigning all the images to the mean.
Then it creates a mean of the images after the second pass, where the mean is
in alignment with the first image.
>
> If I need to actually do 2 separate realignment passes (and select two
> realignment - estimate and reslice options, one at a time), do I
> 1) initially select all my images, change the number of passes
> to "register to first" and reslice a "mean image only".
> 2) input my images again (adding the mean image as the very first image)
> and select estimate and reslice again, only this time select "register to
> first" and reslice "images 2...n"?
You shouldn't need to do anything extra like this.
Note that if you enter multiple sessions (runs) for a subject, then it will do
something slightly different.
Best regards,
-John
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