[log in to unmask]">I think this design is limited to comparing the conditions and not comparing a specific condition against 0.

As you pointed out, if say cond1 = 10 cond2= 12 cond3 = 15 then your constant (implicit baseline if you wish) is 10.5 and the effect of A is -0.5, B = 1.5 and C 9.5. Now if cond1 = 10 cond2= 12 cond3 = 12, then the constant would be smaller AND, A would be less negative. Thus comparing the effect of A against 0 depends on the other conditions values, as such comparing A against 0 should not be done as its not interpretable. In both cases though, A-B=2.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Wed, Jul 10, 2013 at 6:01 AM, cyril pernet <[log in to unmask]> wrote:

Re Yann

Hi Cyril,

Thanks for your reply. However, I should be more specific...

The model here is "fully-specified", ie there is no baseline ( blocks of rest or fixation cross) in this experiment, 1 session (= 1 instruction) is made of following blocks representing the 3 conditions, each repeated 3 times.

The whole experiment can be represented like:

session1 = inst1( block cond1, block cond2, block cond3; block cond1, block cond2, block cond3; block cond1, block cond2, block cond3)

session2 = inst2( block cond1, block cond2, block cond3; block cond1, block cond2, block cond3; block cond1, block cond2, block cond3)

session3 = inst3( block cond1, block cond2, block cond3; block cond1, block cond2, block cond3; block cond1, block cond2, block cond3)

Therefore, if we want to look at the effect of cond1, what will be considered as "implicit baseline"? Because it cannot be nothing ... Will SPM be able to average something within a session? Within the whole experiment (3 sessions concatenated)?

the constant term of the design matrix is the adjusted mean that is the mean minus all of the other effect so if say cond1 = 10 cond2= 12 cond3 = 15 then your constant (implicit baseline if you wish) is 10.5 and the effect of A is -0.5, B = 1.5 and C 9.5 --- it doesn't really matter what adjusted mean you end up (depending on the model) with, the relationship between A B C will be kept so back to your contrast getting A, B, C then group testing should be fine - but if you have a strong hypothesis for an effect like A vs B and A vs C then best is to compute this per subject and the group level on those contrast

cyril

Thanks again,

Best,

Yann

On 10/07/2013, at 4:16 PM, Dr Cyril Pernet wrote:

It will be the average of what is NOT modelled by the instruction / condition regressors and thus 010000 is testing if condition 1 > baseline differs from 0

Sent from my mobile phone

Dr Cyril Pernet
Brain Research Imaging Centre
www.sbirc.ed.ac.uk/cyril/


----- Reply message -----
From: "Yann Quidé" <[log in to unmask]>
To: <[log in to unmask]>
Subject: [SPM] Question about implicit baseline
Date: Wed, Jul 10, 2013 03:43


Dear all,

We have a question concerning implicit baseline. In an experiment using a block design, we have 3 different conditions within 3 different sessions (3 different instructions, ie inst1cond1, inst1cond2, inst1cond3; inst2cond1, inst2cond2, inst2cond3; inst3cond1, inst3cond2, inst3cond3), all modelled with no rest or fixation cross, all in the same order across session.

If at the 1st level analysis, I want for example to have a look at the effect of cond1 (say whatever the instruction) and create the vector [1 0 0], what exactly will be my implicit baseline here? Will it be an average of anything occuring during the other conditions (ie an average of what happens in the 0 0 of my [1 0 0] vector)?

Is there anything wrong it that approach?

Thanks in advance for your thoughts.

Best,

Yann
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

-- 
Dr Cyril Pernet,

Academic Fellow
Brain Research Imaging Center
http://www.bric.ed.ac.uk/
Division of Clinical Neurosciences
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU
Scotland, UK

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