Hi all,
ideally you might even want to estimate your GLM on K-space time series
data, because that's were the actual temporal sampling order is 'exact'.
And finally reconstruct the parameter maps to real space, as is usually
done in realtime during scanning for raw data.
Not sure how much that improves your results though, with a sluggish or
badly modeled HRF...
I think I read a paper on that once, but I cannot find the reference
right now.
Just a thought.
Bas
Torben Ellegaard Lund schreef:
> 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
> [log in to unmask]
>
> 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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