Dear Yiquan
The following mail from Stefan Thesen describes how this information
is found on siemens data:
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind03&L=SPM&P=R435543
I completely agree with John, a slice specific design matrix would be
better from some aspects, but if the data are not corrected smoothing
becomes less trivial :-)
Hope this helps
Torben
Torben Ellegaard Lund
Assistant Professor, PhD
The Danish National Research Foundation's Center of Functionally
Integrative Neuroscience (CFIN)
Aarhus University
Aarhus University Hospital
Building 30
Noerrebrogade
8000 Aarhus C
Denmark
Phone: +4589494380
Fax: +4589494400
http://www.cfin.au.dk
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Den 07/01/2009 kl. 16.25 skrev John Ashburner:
> Slice ordering is something that your local physicists may be able
> to advise
> on. Some (most??) manufacturers do not actually save the slice
> order in the
> DICOM files produced by the scanner. It is therefore not possible to
> automatically encode the slice order in the NIfTI headers (even
> though there
> is space to write such information).
>
> I never actually do any fMRI analysis, but was wondering what the
> expert view
> would be if this option was removed in SPM8. From a generative
> modelling
> perspective, the design matrix, rather than the data, should be
> adjusted to
> account for different acquisition times (i.e., to maximise the
> probability of
> the data given the model).
>
> Best regards,
> -John
>
> On Wednesday 07 January 2009 14:35, s yq wrote:
>> Dear users,
>>
>> Would some one please tell me that from where can I read the slice
>> acquisition order is ascending (1,2,3...), descending(23,22,21...) or
>> interleaved, (1,3,5... 2,4,6) and the Reference Slice is which slice?
>>
>> I used MRIcro to open the dicomed hdr file (Header - open head),
>> and then
>> click Header - information, however only can see the TR, TE, time
>> and so on
>> there in the notes.
>>
>> Best regards
>> Yiquan
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