Dear SPM & GLM Flex experts,
I updated my previous question. The question now incorporates my first draft to set up a design using glm flex. I hope this way my questions become more specific – thanks in advance.
I’m using GLM flex to model a complex study design. Briefly, we applied a pharmacological treatment vs. placebo to healthy volunteers before they underwent an emotional face task with different emotional categories. Moreover, we are interested in the specific interaction effects of the participant’s gender & the gender of the facial stimuli. This gives us a complex design with the following factors:
Between subject factors
1.) Treatment (2 levels (treatment (TR) vs. placebo (PL))
2.) Participants gender (2 levels (male (P_M) vs. female (P_F))
Within subject factors:
1.) Emotional condition (5 levels (Hap, Ang, Fea, Sad, Dis))
2.) Stimulus Gender (2 levels (male faces (S_M) vs. female faces (S_F))
I used the following commands in GLM Flex to create the corresponding design:
IN.N_subs = [8 9 10 11]; % first between factor ‘Treatment` (labels ‘PLC’, ‘TR’), second between subject factor ‘participant gender’ (labels 'P_F', 'P_M')
>>Question: how is the order of the 4 experimental groups defined? I used the following order of groups ‘PLC P_F’ ‘PLC P_M’ ‘TR P_F’ ‘TR P_M’ – correct?
IN.Between = [2 2]; % between factors – ‘treatment’ & ‘participant gender’
>> Question: the GLM Flexed mixed design example uses the additional within factor ‘ALL’. Is it recommended to include this factor in my design as well?
IN.BetweenLabs = {{'PLC', 'TR'} {'P_F', 'P_M'}}; % first factor ‘treatment’ levels ‘PLC’ & ‘TR’; second factor ‘participant gender’ levels 'P_F' & 'P_M'
IN.Within = [5 2]; % within factors ‘emotional category’, ‘stimulus gender’
IN.WithinLabs = {{'HAP', 'ANG', 'FEA', 'SAD', 'DIS'} {'S_F', 'S_M'}}; % first factor ‘emotional category’ levels 'HAP', 'ANG', 'FEA', 'SAD', 'DIS'; second factor ‘stimulus gender’ levels 'S_F' & 'S_M'
IN.FactorLabs = {'TREATMENT' 'P_GENDER' 'EMOTION' 'S_GENDER'}; %factor labels
>> Question: labels have been added in the order: 1 between subjects factor / 2 between subject factor / 1 within subject factor / 2 within subject factor - Is the order correct?
>> Do I need to specify the factor ‘Subjects’ since the design incorporates repeated-measures within subject factors?
IN.EqualVar = [0 0 0 0 ]; %equal variances 1, unequal 0
>> Question: Is it reasonable to assume unequal variances for all factors?
IN.Independent = [1 1 0 0 ]; %independent 1, dependent 0
>> Question: I assume independence for the between subject factor / dependence for the within subject factors – is this valid?
IN.Interactions = {[1 2]}; % start simple with just one interaction
>> Question: Generally I would like to explore all main effects and interaction effects in the design – do I need to specify all possible 2-way and higher order interactions?
F = CreateDesign(IN);
figure(20); imagesc(F.XX); shg %displays design matrix
>> Question: how to specify the order of scans in the input file list? I have 10 scans per subjects and 2 between subject factor treatment (‘PLC’ vs. ‘TR’) & participant gender (‘P_F’ vs. ‘P_M’) I assume that the order of groups should be
PLC__P_F
PLC__P_M
TR__P_F
TR__P_M
Within each group the order of contrasts should be (example PLC__P_F):
PLC__P_F_SUB_01_HAPP_S_F
PLC__P_F_SUB_01_HAPP_S_M
PLC__P_F_SUB_01_ANG_S_F
PLC__P_F_SUB_01_ANG_M_F
PLC__P_F_SUB_01_FEA_S_F
PLC__P_F_SUB_01_FEA_M_F
PLC__P_F_SUB_01_SAD_S_F
PLC__P_F_SUB_01_SAD_M_F
PLC__P_F_SUB_02_DIS_S_F
PLC__P_F_SUB_02_DIS_M_F
……….
PLC__P_M_SUB_01_HAPP_S_F
PLC__P_M_SUB_01_HAPP_S_M
PLC__P_M_SUB_01_ANG_S_F
Are the contrasts assigned to the correct cells of the design matrix if I use this Input file list?
Thanks in advance & best regards,
Ben
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