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?
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.
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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