The correct way to specify your fMRI design matrix is to specify
either 1 or 2 conditions.
with one condition you just specify the task onsets or with 2 conditions you
specify the task and the rest conditions. SPM people recommend not specifying
the rest condition as it is implicit, however, its always good to run your data
both ways.
SO:
sessions 6
conditions replicated Yes
are timing/parameters the same (YES if you are not using the motion correction
parameters in your statistical design or NO if you will be using them)
conditions (1 or 2)
epoch boxcar
convolve with hrf? (your choice)
other regressors, select 1 and then right click underneath the imput box and go
and find your realignment txt file for each subject if you choose to put these
in your design matrix.
when your results are ready if you want to look at your SPM's there are 2 ways
of looking at your data. to look at the total activations (task)-the total
deactivations(rest) it is specified as such (in your example you put rest
first).
TOTAL
-1 1 -1 1 -1 1 -1 1 -1 1 -1 1 (6 subjects, no motion correction regressors)
Conjunctions (areas that are active in all subjects (ie. intersection))
specify each subject separately
-1 1 0 0 0.......
0 0 -1 1 0 0 ....
0 0 0 0 -1 1 0 0....
etc..
and then use the Ctrl button to select all 6 individual contrasts.
the setup is exactly the same if you decide to use the motion parameters as a
regressor, just add 6 0's between each subtraction
-1 1 0 0 0 0 0 0 -1 1 0 0 0 0 0 0 -1 1 ..........etc.
good luck, sophie
Quoting John Ashburner <[log in to unmask]>:
> would you confirm that I am proceeding correctly here.
>
> I simply want to average data from 6 subjects. The experimental design
> is a simple epoch related set up with 40 secs of fixation (rest)
> followed by 40 of watching a driving scene. This is repeated 4 times
> (i.e. rest --task---rest etc)
> T average the data:
>
> I choose the frmri models
> Select specify and estimate a model
> For the number of conditions I enter 6 (to reflect the number of
> subjects. Is this correct?
I don't really know this part of SPM. I've never done an fMRI
analysis in my life (except during our annual SPM course), so I'm
not sure what questions that get asked. Reading through Karl's
code (spm_fmri_spm_ui.m), it looks like you should have entered
6 for the number of sessions. I don't see any mention of number of
conditions in the SPM99 matlab code though.
> My second question relates to the correct contrast to use in looking at
> the results
>
> To identify the activation associated with the driving scene relative to
> baseline, do I simply enter 1 1 1 1 1 1 or, is it 1 1 1 1 1
> 1-1-1-1-1-1-1 in the contrast dialogue box? I think it is the former.
This depends on what the design matrix looks like, and what each column
represents. The correct contrast could be [1 1 1 1 1 1], but I'm not
sure.
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
--
Sophie Lafaille, B.Sc.(Hons.), M.Sc.
Research Officer II, Speech Fluency Laboratory 1059
Graduate Department of Speech-Language Pathology
500 University Avenue, Toronto, Ontario, Canada M5T 2S8
Ph. 1-(416)-946-8635 Fax 1-(416)-978-1596
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