thanks!!!
livio
> Hi Livio,
>
> On Sat, 5 Mar 2005, Livio Finos wrote:
>
>> Hi Steve,
>> I' sorry to disturbing you again. I have 2 more doubt about the first
>> level analysis setting.
>
>> 1. for each single subject I have 5 scans (3 secs/scans) under cond A
>> and 5 under cond B (repeated 8 times, hence 40 scans for cond A and 40
>> for B).how should I set the Design? If I use the wizard: simple model
>> setup (setting to 15 the A and B period), it seems to me that the
>> contrast doesn't work fine: am I subtracting A-B or just A? I mean, am
>> I asking if cond A is greater than B or am I simply asking if A is
>> greater than 0? Indeed, by looking on the "contrast & F-test" window
>> the contrast for the Ev1 is 1 and no mention is made to the condition
>> B.An alternative way to analyse the data could be to performe 2 one
>> sample t-test for each subjects (A and B condition) as show
>> athttp://www.fmrib.ox.ac.uk/fslcourse/lectures/fmri/s_4120_eg3.htm and
>> (better because we do not assume equal variance between subjects)
>> using a mixed model
>> athttp://www.fmrib.ox.ac.uk/fslcourse/lectures/fmri/_4166_featdirs.fpd/index.htmlthis>> (I suppose) could be done only after creating 2 4D images (40 scans)
>> for each subjects, let say sub##A and sub##B. In this case it seems to
>> me I could have some problem in the registration/normalization phase,
>> since the 40 scans are not sequential (they has been registered 5 by
>> 5, each 5 scans under A there are 5 under B that have been stored to
>> the sub##B image).
>
> Hi - you only have two conditions and not a separate rest condition, so
> you must consider one of the conditions as "rest" - you can only
> compare between the conditions, and not "greater than 0" etc. Hence
> what you are getting from the wizard is probably correct. So if you
> call A "rest" then the [ 1 0] contrast shows B-A and if you add a [-1
> 0] contrast then this shows A-B. Note that the 0 in these contrasts
> just tells FEAT to ignore the temporal derivate EV when forming
> contrasts.
>
>> 2. As you suggested, I'm now using raw data. In the "Data" window I
>> select the initial 10 images (20 if I will use separate image for A
>> and B condition as discussed before). Let call it RAW01,
>> RAW02,...,RAW10. How to set the "registration" window (in the first
>> level analysis)? what should I get in the "initial structural image",
>> "Main structural image" and "Standard Space" (at the moment I'm
>> setting avg152T1_brain.hdr for the latter).In the "pre-stats" I'm
>> setting motion correction=MCFLIRT, BET=ON and smooth=8mm. is it ok?
>
> In the input data selectiong you must choose (for a single session
> analysis) a single 4D image containing ALL of the A and B scans (in the
> right temporal order inside the file!). You can create 4D files from
> multiple 3D files using avwmerge.
>
> Registration is a separate issue - this is described in detail at
> http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#reg
>
> Good luck!
>
> Cheers, Steve.
>
> --
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
>
> 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
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