Dear Michael,
realignment will account for movement within each session, but also
between sessions. All images of all sessions should be in register after
running realignment.
Volkmar
Michael Froelich schrieb:
> 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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