Hi,
On 17 Oct 2006, at 22:29, Jonathan Hakun wrote:
> Hello,
>
> I am working with a sample composed of 18 subjects, each with 1 scan
> session. The paradigm I've been modeling is a block design with 16
> total
> blocks: 8 individual activation blocks being modeled separately (8
> individual activation blocks that we want to later weigh, and run some
> covariates against; so each is being modeled as a separate EV), and
> another
> 8 blocks (the neutral condition) which are being modeled as 1 EV,
> as we can
> see no need to break these into 8 individual EVs.
>
> Question #1: Is it safe to assume that modeling all 8 Neutrals
> together
> (denoted in 1 stick file -- unlike the 8 individual activation blocks
> denoted in 8 different stick files) is similar enough to the
> activation
> blocks which are each model separately, such that we can adequately
> define a
> contrast of each activation block minus neutral in the 1st level
> contrast.
> Or is the EV of Neutral being modeled much more profoundly b/c it
> consists
> of 8 blocks versus the activation blocks being 1 block each?
It certainly doesn't matter that the "neutral" condition includes
more timepoints than the activation blocks - the differential
contrasts are not biased by this.
Though I do have a question - do you also have separate "rest"
conditions to the neutral? If not, then in effect your neutral is the
"rest", in which case, as the data and model are demeaned at first
level, then you should simply exclude the neutral covariate. Then you
would simply discard contrasts 10-17; their questions would be
covered by 1-8.
> This design, in a nutshell looks like this:
> (note: "Block_of_interest" = "activation block")
>
> 9 EVs in the 1st level:
> Block_of_interest1 (BOI1_stick)
> Block_of_interest2 (BOI2_stick)
> Block_of_interest3 (BOI3_stick)
> Block_of_interest4 (BOI4_stick)
> Block_of_interest5 (BOI5_stick)
> Block_of_interest6 (BOI6_stick)
> Block_of_interest7 (BOI7_stick)
> Block_of_interest8 (BOI8_stick)
> Neutral(8blocksin1)(NTL_stick)
>
> BOI1 through 4 are the "low saliency activation blocks" and BOI5
> through 8
> are the "high saliency activation blocks."
>
> My Matrix for Contrasts at the 1st level looks like this:
> EV1 EV2 EV3 EV4 EV5 EV6 EV7 EV8 EV9
> C1_BOI1 1 0 0 0 0 0 0 0 0
> C2_BOI2 0 1 0 0 0 0 0 0 0
> C3_BOI3 0 0 1 0 0 0 0 0 0
> C4_BOI4 0 0 0 1 0 0 0 0 0
> C5_BOI5 0 0 0 0 1 0 0 0 0
> C6_BOI6 0 0 0 0 0 1 0 0 0
> C7_BOI7 0 0 0 0 0 0 1 0 0
> C8_BOI8 0 0 0 0 0 0 0 1 0
> C9_NTL 0 0 0 0 0 0 0 0 1
> C10_BOI1-Ntl 1 0 0 0 0 0 0 0 -1
> C11_BOI2-Ntl 0 1 0 0 0 0 0 0 -1
> C12_BOI3-Ntl 0 0 1 0 0 0 0 0 -1
> C13_BOI4-Ntl 0 0 0 1 0 0 0 0 -1
> C14_BOI5-Ntl 0 0 0 0 1 0 0 0 -1
> C15_BOI6-Ntl 0 0 0 0 0 1 0 0 -1
> C16_BOI7-Ntl 0 0 0 0 0 0 1 0 -1
> C17_BOI8-Ntl 0 0 0 0 0 0 0 1 -1
> C18_AllLow 1 1 1 1 0 0 0 0 0
> C19_AllHigh 0 0 0 0 1 1 1 1 0
> C20_AllLow-AllHigh 1 1 1 1 -1 -1 -1 -1 0
> C21_AllHigh-AllLow -1 -1 -1 -1 1 1 1 1 0
>
> Question #2 for the 1st level: Now, another question on the 1st
> level was
> whether it was statistically legal to model the "all low" and the
> "all high"
> contrasts the way I did. Is it reasonable to add 4 betas together
> in a
> contrast like this? Or should the "all low" line have looked like
> this:
>
> All Low .25 .25 .25 .25 0 0 0 0 0
>
> I was having a hard time understanding whether a contrast had to
> add up to 1
> or 0, or not, and in which situations it did not have to.
Indeed - it doesn't matter in terms of the 1st-level tstats that you
will get out from this - scaling a contrast doesn't affect the
resulting t-stat. However, if you are going to then contrast this
contrast with another at a higher-level, you need to make sure that
their absolute scaling is comparable - the easiest way to be safe is
to follow your suggest of using 0.25 instead of 1 as this then means
that the contrast is giving the "mean" effect.
I think given my previous comments above it would be simpler to get
the first-level queries sorted first, before I embark on the second-
level questions - so maybe you can re-submit the 2nd levels questions
in the light of my answers above?
Cheers, Steve.
> 2nd Level:
>
> When I bring this data to the 2nd level, in order to model for
> "BOI1-Ntl",
> etc, for the group, I had brought up the COPEs for every subject
> (all 18
> subjects) for each BOI-Ntl contrast (8 contrasts-C10 through C17:
> BOI1-Ntl,
> BOI2-Ntl, ..., BoI8-Ntl). I did this in order to evaluate the group
> contrast of a given BOI versus neutral, i.e. to see activation on
> the group
> level corresponding directly to each activation block less the
> value of the
> neutral stimulus. We'll forgoe looking at the data from the 1st
> level that
> I had a question about (i.e. C19_AllHigh or C18_AllLow) as I'm not
> certain I
> adequately modeled this correctly, and I did not want to bring it
> up to a
> group level until I was certain I had it right on the 1st level).
> So for
> now just the 8 copes Copes10-17.
>
> The model on the 2nd level looks like this:
>
> EV's (copes from 1st level 8 per subject by 18 subjects):
> EV1 EV2 EV3 EV4 EV5 EV6 EV7 EV8
> Subj1_Cope10 1 0 0 0 0 0 0 0
> Subj1_Cope11 0 1 0 0 0 0 0 0
> Subj1_Cope12 0 0 1 0 0 0 0 0
> Subj1_Cope13 0 0 0 1 0 0 0 0
> Subj1_Cope14 0 0 0 0 1 0 0 0
> Subj1_Cope15 0 0 0 0 0 1 0 0
> Subj1_Cope16 0 0 0 0 0 0 1 0
> Subj1_Cope17 0 0 0 0 0 0 0 0
> Subj2_Cope10 1 0 0 0 0 0 0 0
> Subj2_Cope11 0 1 0 0 0 0 0 0
> Subj2_Cope12 0 0 1 0 0 0 0 0
> Subj2_Cope13 0 0 0 1 0 0 0 0
> Subj2_Cope14 0 0 0 0 1 0 0 0
> Subj2_Cope15 0 0 0 0 0 1 0 0
> Subj2_Cope16 0 0 0 0 0 0 1 0
> Subj2_Cope17 0 0 0 0 0 0 0 1
> Subj3_Cope10 1 0 0 0 0 0 0 0
> Subj3_Cope11 0 1 0 0 0 0 0 0
> ...
> ...
> ...and so on
>
> I do this in order to bring all the copes for BOI1-Ntl up to the
> group level
> where I can make a contrast of "groupmean_BOI1-Ntl" "groupmean_BOI2-
> Ntl" and
> so on.
>
> So in my contrast page I define things like:
> EV1 EV2 EV3 EV4 EV5 EV6 EV7 EV8
> C1-gm_BOI1 1 0 0 0 0 0 0 0
> C2-gm_BOI2 0 1 0 0 0 0 0 0
> C3-gm_BOI3 0 0 1 0 0 0 0 0
> C4-gm_BOI4 0 0 0 1 0 0 0 0
> C5-gm_BOI5 0 0 0 0 1 0 0 0
> C6-gm_BOI6 0 0 0 0 0 1 0 0
> C7-gm_BOI7 0 0 0 0 0 0 1 0
> C8-gm_BOI8 0 0 0 0 0 0 0 1
> C9-gm_AllLow-Ntl 1 1 1 1 0 0 0 0
> C10-gm_AllHigh-Ntl 0 0 0 0 1 1 1 1
> C11-gm_(Low-Ntl)-(High-Ntl) 1 1 1 1 -1 -1 -1 -1
> C12-gm_(High-Ntl)-(Low-Ntl) -1 -1 -1 -1 1 1 1 1
> C13-gm_ALLBOI-Ntl 1 1 1 1 1 1 1 1
>
> Question 3: Now, same quesion about C9 and C10. Was I allowed to
> define a
> contrast that added up to 4? I didn't feel comforted by this.
>
> Question 4: When evaluating C13, I asked whether I could have a
> contrast add
> up to 8. I want to see the value of ALL the BOI's minus Neutral.
> Since
> each BOI minus neutral was carried out as COPE10-17 on the 1st
> level, I was
> hoping I could somehow make a contrast on the 2nd level that would
> depict
> ALL BOI-neutral by bring them up and averaging them somehow. I
> also tried
> this in a 2nd pass at this data as C14:
>
> C14-gm_ALLBOI-Ntl .125 .125 .125 .125 .125 .125 .125 .125
>
> This way the contrast adds up to one, giving 1/8 weight to each
> contrast.
> Peculiar thing, is that the results are identical (at least they
> appear to
> have the same range of Z-scores, and appear to be identical z-maps.
>
> So again the major questions here have to do w/ generating
> contrasts. 1)
> Can the contrast add up to something other than 1 and why or why
> not? 2)
> Does this 2nd level model I've drawn up seem to be a reasonable way to
> generate a group map for BOI's individually minus neutral, and then
> again as
> ALL BOI minus neutral. Is weighing the contrast as 1/8 each the
> correct
> modification to the contrast to see ALL_BOI-Ntl? 3) Also, might I
> instead
> carry out a 3rd level analysis, where each of C1-8 from the 2nd
> level is
> defined as 1 single EV where a 3rd level contrast shows the
> positive 1 value
> of that EV for the group...would that look exactly the same as my
> C13 or C14?
>
> Thank you in advance for glancing at these models. I'm not new so
> much to
> modeling fMRI data, as a I am to FSL. I've typically worked w/
> SPM, and the
> conversion is stumping me from time to time.
>
> After someone digests this, I have a question about modeling
> correlations
> based on the contrasts I've generated at the 2nd level. I'll ask
> this in
> another string.
>
> ~Jonathan
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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