Dear Amy,
I'm a little puzzled by your questions.
It is normal that a stimulus repeats - i.e. on, off, on, off, on, off , etc.
So there is no need to put any Stop after value.
I assume that your stimuli are also repeating - if not, then you will have
some serious problems with getting enough statistical power, as one
block is a very weak design.
So if you have condition A that is on for 25s then off for 175s then
on for 25s, then off for 175s, etc., then you can set this up with a
square wave design with On=25, Off=175, Phase=175 (to make it
start with an On period). Then condition B would be the same but
with Phase=125 (as it is 50 seconds later than condition A). You
could do this also with a non-zero Skip, but I think it is better not to.
Also, keep Stop After at -1, since you just want it to repeat like the
stimulus (at least I hope so, as otherwise you will have real trouble
getting power out of your experiment).
There is no need to change the default convolution parameters unless
you have some special group of subjects with unusual haemodynamics.
As for the high-pass filter, in a design like this you can just set it to the
period of each condition, which is 200 seconds. You can probably also
get away with the default (100) - and you can check this by viewing
the design matrix with both settings of the high-pass filter and seeing
if there is much of a difference. If there is a difference then that indicates
that the filter is filtering out some of your experimental power, which is
not what you want.
All the best,
Mark
On 21 Dec 2010, at 03:32, Amy Zhong Sheng Zheng wrote:
> I completed the AV data practical and have looked around on the fsl webpage quite a bit, but some didn't seem completely clear to me. I followed the manual from the feat webpage below:
> "If you have chosen a Square or Sinusoid basic shape, you then need to specify what the timings of this shape are. Skip is the initial period of zeros (in seconds) before the waveform commences. Off is the duration (seconds) of the "Off" periods in the square wave. On is the duration (seconds) of the "On" periods in the square wave. Period is the period (seconds) of the Sinusoid waveform. Phase is the phase shift (seconds) of the waveform; by default, after the Skip period, the square wave starts with a full Off period and the Sinusoid starts by falling from zero. However, the wave can be brought forward in time according to the phase shift. Thus to start with half of a normal Off period, enter the Phase as half of the Off period. To start with a full On period, enter the same as the Off period. Stop after is the total duration (seconds) of the waveform, starting after the Skip period. "-1" means do not stop. After stopping a waveform, all remaining values in the model are set to zero."
>
> The AV practical mentioned:
>
> • Setup EV1 (the visual stimulation timing): set Off to 30, On to 30 and Phase to 30. This describes a square wave of total period 60s. It starts with an ON period, hence the phase setting, which shifts the waveform forward in time.
> • Setup EV2 (the auditory stimulation timing): set Off to 45, On to 45 and Phase to 45. This describes a square wave of total period 90s.
> My question is (referring to the av practical), should I assume that for EV1, when mentioning the "square wave of total period 60s", the "Stop after (s)" should be changed from -1 to 60s, and for EV2, to 90s? Also, when setting up EV2, should it skip 60s (since this period covered the visual stimulation), then set off to 45, on to 45, phase to 45, so forth?
>
> Thanks very much,
>
> Amy
>
> On Mon, Dec 20, 2010 at 5:16 PM, Mark Jenkinson <[log in to unmask]> wrote:
> Dear Amy,
>
> Almost all of these questions are answered in the FSL course practical on FEAT:
> http://www.fmrib.ox.ac.uk/fslcourse/
> I advise you to do the first practical exercise there (with the AV data) as this will
> teach you how to set these parameters up (when coupled with reading the FEAT
> webpage documentation).
>
> All the best,
> Mark
>
>
> On 21 Dec 2010, at 00:56, Amy Zheng wrote:
>
> > Hi all,
> >
> > I have a block design with 4 different conditions, and I'm trying to figure out how to properly set up the model. It starts with an ON period of 25s then alternates with OFF 25s, etc; so, Condition A, Rest, Condition B, Rest, Condition C, Rest, Condition D, Rest, total lasting about 200s.
> >
> > I'm running the first-level analysis and in the full model setup I put 4 EVs, with basic Square shape and Gamma Convolution.
> > For the 1st EV:
> > Skip (s)=0
> > Off (s)=25
> > On (s)=25
> > Phase (s)=25
> > Stop after (s)=50? (I'm tempted to put 50s, as in 25s On+25s Off for each condition, or should I leave it as -1?)
> >
> > For the 2nd EV:
> > Skip (s)=50?
> > Off (s)=25
> > On (s)=25
> > Phase (s)=25?
> > Stop after (s)=50?
> >
> > For the 3rd EV:
> > Skip (s)=100?
> > Off (s)=25
> > On (s)=25
> > Phase (s)=25?
> > Stop after (s)=50?
> >
> > For the 4th EV:
> > Skip (s)=150?
> > Off (s)=25
> > On (s)=25
> > Phase (s)=25?
> > Stop after (s)=50?
> >
> > ALSO, should I change the default "Stddev and Mean lag" values under the Gamma Convolution option, which are 3, and 6 s, respectively? Another question is: how does one determine what high pass filter value to use?
> >
> > Thanks,
> > Amy
> >
>
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