Dear Steve,
I have processed our subjects for this experiment to the point of having
combined the three sessions for each subject. We have two groups of subjects
(n=6 in each); what would be the best way of proceeding to a group
comparison?
Many thanks again for your help,
Xavier
-----Original Message-----
From: Xavier Chitnis [mailto:[log in to unmask]]
Sent: 18 September 2001 15:28
To: [log in to unmask]
Subject:
Hi.
Indeed - although FEAT lets you run lots of first-level analyses from a
single setup and push of the "GO" button, you can only do this if the
design matrix is the same for all analyses - not the case here.
Both of your suggestions are fine, although there are practical downsides
to concatenation, so we do not reccomend that in general.
Thus - you should carry out each first-level analysis separately. You
should obviously make sure that EV1 corresponds to the same stimulus type
in each analysis etc. - otherwise second-level analyses will not be able
to relate EV1 from session 1 to EV1 in session 2 etc.
You can then do simple group stats using FEAT to combine the first-level
analyses from the different sessions for a single subject. Note that FEAT
cannot yet (though watch this space!) do third-level (etc) analyses so
it's not very easy to THEN do group stats across subjects - if you do want
to do this, then there is a workaround - a fairly simple way of achieving
simplified fixed-effects analyses at any number of levels which we could
explain.
Thanks, Steve.
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
On Fri, 7 Sep 2001, Xavier Chitnis wrote:
> Dear Steve,
>
> Thank you very much for your help. I have one more question....
>
> The task consists of three sessions for each subject. The order of the 4
> types of stimuli (ABCD) is different across the three runs. In running one
> subject through FEAT, I selected a full first level analysis for 3
volumes,
> and then selected one session for each volume. However, because the order
of
> the stimuli is different across the three sessions, I cannot tell FEAT
what
> the order is for each session, as I think it assumes that they are the
same
> for each session.
>
> I have considered two approaches to this. Firstly, to set up and analyse
> each session separately. Alternatively, to concatenate the three sessions
> into one very large session, and analyse it that way. Is either of these
> appropriate, or is there a better way?
>
> Many thanks
>
> Xavier
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On
> Behalf Of Stephen Smith
> Sent: 06 September 2001 17:23
> To: [log in to unmask]
> Subject: Re: [FSL] FEAT
>
>
> Aha - good - so in fact all your scanning IS regular, and my initial
> worries are gone.
>
> So - to your original questions:
>
> >>>>
> I set up the analysis (for a single subject as follows). I selected a full
> model setup. Given that there are 4 active conditions, I selected 4 EVs.
> For the basic shape, I selected Custom (1 entry per volume). I then
> created 4 text files, one for each of the active conditions. In each text
> file, I used 1 to specify images relating to that active condition, and 0
> for every other image.
> >>>>
>
> this is fine - though it might have been easier to simply specify the
> activation periods (seconds) for each EV type in 3-column format text
> files. the result should be the same.
>
> >>>>
> For the contrasts, I looked for activations in each of the active
> conditions (by selecting 1, and 0 for all the others)
> >>>>
>
> this is fine too - and if you want to compare conditions, use [1 -1] type
> contrasts.
>
> Sorry for the confusion - hope it gives the activation you want!
>
> Thanks, Steve.
>
> Stephen M. Smith
> Head of Image Analysis, FMRIB
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
Xavier Chitnis MSc.
Division of Psychological Medicine
Institute of Psychiatry
London, SE5 8AF
Tel: 020 7848 0541
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