Hi,
>I am strating using FSL under the recomendation of Dr. Stephen Strother. I
>have some questions.1), i have a 16 slice/volume scan, the order is
>ascending and interleaved from 3T Whole Body MR System (MAGNETOM Trio,
>Siemens Medical Systems,Erlangen,Germany). I produced a order file like
>this: 1 9 2 10 3 11 4 12 5 13 6 14 7 15 8 16. I am wondering if it is
>correct.
Apologies, I don't know this
> 2) I have a millisecond protocal file for each subject from
>Brainvoyage. Is there any way to use the info to define the model in FSL in
>some simple way?
>3) If i am only
>interested in the comparison of two evs, should i only define these two evs
>and left the rest scan blank or should i define a full model for each scan?
>4) should i define each ev as 1 and set contrast to get the effect i want?
>How should i define baseline ev? 0 or -1?
You will need to convert it so that it is compatible with FSL's one column
or three column format for entering stimulus timings. Take a look at the
Stats-EVs section on http://www.fmrib.ox.ac.uk/fsl/feat5/index.html for a
description. This describes the stimulus timings, which then gets
convolved with the HRF (which you can define on the Feat GUI in a variety
of ways - if you don't want any convolution you can turn it off).
Note, that the EVs that you setup will be demeaned for you (as is the
data) before the GLM is fitted.
I am not clear from you description what conditions you have, e.g. what
different experimental conditions, what is your baseline, is rest your
baseline, do you have any rest periods? However, assuming that you do have
rest, all EVs representing experimental conditions (HRF convolved
stimulus) should be with respect to rest - and you should then NOT have a
separate EV representing the rest condition (otherwise the design would be
rank defficient).
--
Cheers, Mark.
Mark Woolrich.
Oxford University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
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