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Subject:

Re: contrasts

From:

Richard Perry <[log in to unmask]>

Reply-To:

Richard Perry <[log in to unmask]>

Date:

Mon, 11 Jan 1999 11:10:18 +0100

Content-Type:

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Dear Dr Nijland,

>but what contrast do i have to use to show the difference in activation
>between for example activation 1 and activation 2 and what contrast should i
>use to show the parts of the brain activated by both activation1 and
>activation 2 ?

If the rows in your design matrix are ordered rest, activation 1,
activation 2, activation 3, then...

0, 1, -1, 0 will show the 'difference in activation between activation 1
and activation 2', but you should be aware that voxels may be shown up
which do not show up in the contrast -1, 1, 0, 0 (activation 1 vs rest).
The reason for this is that there may be voxels which show, for example,
the same signal at rest and in activation 1, but less signal in activation
2.

If by 'difference in activation' you are asking which voxels give more
signal in activation 1 than at rest, but do not give more signal in
activation 2 than at rest, then this is a different question, as was made
clear by the answers to Thomas Stephan's question on the 17th December,
which I have added to the bottom of this e mail.

To show voxels which give more signal in activation 1 than at rest, AND
show more signal in activation 2 than at rest, you could mask the contrast
-1, 1, 0, 0 with the contrast -1, 0, 1, 0.

Best wishes,

Richard Perry.


Dear Thomas,
>
>we have a question regarding the contrast setup for the fmri statistic:
>Our experiment has 3 Conditions: Rest, Stim1 and Stim2.
>We build contrasts like this:
>C1: -1  1  0  to see effects of Stim1 against Rest condition
>C2:  1 -1  0  to see negative effects of Stim1 against Rest
>C3: -1  0  1  to see effects of Stim2 against Rest condition
>C4:  1  0 -1  to see negative effects of the above
>C5:  0  1 -1  to see effects of Stim1 that can not be explained through
>              Stim2.
>
>Now the question:
>Does contrast 5 give me the areas activated by stimulus1 that are not
>activated by stimulus2 ?
>How can I see the negative effects corresponding to contrast5 ?
>

The answer to your second question is straightforward: the contrast must be
0 -1 1.
However, I am not sure that your description of contrast 5 as 'the effects
of Stim1 that can not be explained through Stim2' is entirely clear.

The contrast 0 1 -1 gives you voxels which show significantly more BOLD
signal in the Stim1 epoch than in the Stim2 epoch.  This may be because
there is an increase in BOLD signal in response to Stim1 or because there
is a decrease in BOLD signal in response to Stim2, and your contrasts 1-4
will help you to work out which it is.

Which 'effects of Stim1 ... can not be explained through Stim2' seems to me
to be a (slightly) different question, if by this you mean 'voxels which
show significantly more BOLD signal in the Stim1 epoch than in the rest
epoch, but do not show significantly more BOLD signal in the Stim2 epoch
than in the rest epoch'.  This sort of 'negative conjunction' would yield
an SPM which gives fewer significant voxels than the contrast 0 1 -1,
because it would leave out those which are attributable to a decrease in
BOLD signal in the Stim2 epoch.

Such an SPM could be obtained by masking the contrast 0 1 -1 (to obtain
those voxels which show more BOLD signal during the Stim1 epoch than during
the Stim2 epoch) with the contrast -1 1 0 (so that you only ask this
question of voxels which have more BOLD signal during the Stim1 epoch than
during the rest epoch).  The 'negative effects' would be obtained by
masking the contrast 0 -1 1 (to obtain those voxels which show less BOLD
signal during the Stim1 epoch than during the Stim2 epoch) with the
contrast 1 -1 0 (so that you only ask this question of voxels which have
less BOLD signal during the Stim1 epoch than during the rest epoch).

Perhaps the SPM experts (I am a newcomer to the field) will comment on
whether such an analysis is a meaningful way of presenting the data.
Certainly the usual thing seems to be to present contrast 0 1 -1 and
contrast -1 1 0, so that the reader can tell by eye-balling these, which
clusters are common to both of these SPMs,

Best wishes,

Richard Perry.



Dear Thomas,

> we have a question regarding the contrast setup for the fmri statistic:
> Our experiment has 3 Conditions: Rest, Stim1 and Stim2.
> We build contrasts like this:
> C1: -1  1  0  to see effects of Stim1 against Rest condition
> C2:  1 -1  0  to see negative effects of Stim1 against Rest
> C3: -1  0  1  to see effects of Stim2 against Rest condition
> C4:  1  0 -1  to see negative effects of the above
> C5:  0  1 -1  to see effects of Stim1 that can not be explained through
>               Stim2.
>
> Now the question:
> Does contrast 5 give me the areas activated by stimulus1 that are not
> activated by stimulus2 ?

More exactly it shows areas that are activated by stimulus1 relative
to stimulus2.  Areas that are 'more' activated by stimulus1 implies
that both stimulus1 and stimulus2 activate relative to rest.  These
areas would be identified by the conjunction (or masking of) C5 with
C1 and C3.


> How can I see the negative effects corresponding to contrast5 ?

Simply use

C6:  0  -1 1

With best wishes - Karl




from: Dr Richard Perry BM BCh MA PhD MRCP(UK),
Clinical Research Fellow, Wellcome Department of Cognitive Neurology,
Darwin Building, University College London, Gower Street, London WC1E 6BT.
Tel: 0171 504 2187;  e mail: [log in to unmask]
Pager: 04325 253 566.




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