Volkmar,
the only issue I am wondering about now is the registration of
different sessions to each other.
I understand that the realignment produces the movement parameters
that then can be used as regressors and that takes care of the
movement within a session.
But let's assume that the position of the participant differs slightly
from session 1 to session 2.
Since the co-registration, in my example, was based on aligning the
anatomical image to the first image of session 1 only, how does hat
guarantee that sessions 2, 3 ...
are also coregistered (matched up) with the anatomical image correctly.
For example, if the first image of session 2 is rotated by 1 degree
compared to the first image of session 1, wouldn't the normalization
step
be somewhat off for session 2?
Michael
Michael Froelich, MD MS
E-mail: [log in to unmask]
office: (205) 975-0145
On Jun 25, 2009, at 6:35 AM, Volkmar Glauche wrote:
> Dear Michael,
>
> the procedure you use looks perfectly ok to me. Realigning all
> sessions
> means that all functional images are in register with the first
> image of
> the first session. This image is also the reference in your
> coregistration step - thus registering the anatomical image to the
> functional time series. Therefore, you can apply the normalisation
> parameters from segment to these images (of course assuming that all
> of
> the steps above produced accurate results).
>
> Volkmar
>
> Dear SPMers,
>
> I am unsure about a batch script that I have been using and just
> want to
> make sure what
> I am doing is correct.
>
> I am preprocessing mutisession fMRI data of a block design.
> (1) First, I am obtaining realign parameters ("Realign: Estimate") for
> all sessions for a
> subject.
> (2) Then, I am coregistering the anatomical image (source image). As
> Reference image, I
> am entering my "Realign: Estimate: Realigned Images (Sess 1)" file via
> "Dependency".
> (3) Then, I am segmenting the subject's anatomical image.
> (4) Then, I am normalizing ("Normalize: Write") all sessions using all
> "Realign: Estimate:
> Realigned Images (Sess 1, 2, ...)" as "Images to Write" and the "DEP
> Segment: Norm
> Params Subj->MNI" option as "Parameter File".
>
> Therefore, for the coregistration step, I have used only Session and
> probably just one
> image out of that functional series to coregister with the subject's
> anatomical image.
>
> I am asking naively a few questions:
> As I am apparently only coregistering one image of one session to my
> anatomical image,
> should I be concerned about deformations? Should I not consider
> several
> sessions for the
> coregistration to my anatomical image? Am I correct in the
> interpretation that, at the
> normalization step, the parameters from the normalization of the
> segmentated
> anatomical image are used to normalize my functional (Session) images?
>
> These questions are basically to make sure I understand the process
> correctly.
>
> Thanks,
>
> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?
> A2=ind0906&L=SPM&P=213880>
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