Dear Steve,
I combined the three sessions for each subject using FEAT group statistics - three input volumes per subject, registration & group stats (a single group for each subject)
Many thanks
Xavier
>Hi - I assume you've combined the data using group stats in FEAT - or did
>you use concatenation of the time series' in the end?
>
>Thanks
>
> 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 Tue, 18 Sep 2001, Xavier Chitnis wrote:
>
>> 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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