Dear Freesurfer Mailing List,
I wish to run a GLM in freesurfer with 3 categorical variables
(haplotype-2levels, gender-2levels, group-2levels), and 1 continuous
variables (age). Unfortunately, the MRI images I am using come from five
different testing sites, so I also need to account for the potentially
confounding effects of using different scanners. So my fsgd file like this:
GroupDescriptorFile 1
Title GLM_SiteGender
Class siteBrisbane-numRiskNoRisk-genderMale-groupCase
Class siteBrisbane-numRiskNoRisk-genderFemale-groupCase
Class siteBrisbane-numRiskNoRisk-genderMale-groupControl
Class siteBrisbane-numRiskNoRisk-genderFemale-groupControl
Class siteBrisbane-numRiskanyRisk-genderMale-groupCase
Class siteBrisbane-numRiskanyRisk-genderFemale-groupCase
Class siteBrisbane-numRiskanyRisk-genderMale-groupControl
Class siteBrisbane-numRiskanyRisk-genderFemale-groupControl
Class siteMelbourne-numRiskNoRisk-genderMale-groupCase
Class siteMelbourne-numRiskNoRisk-genderFemale-groupCase
Class siteMelbourne-numRiskNoRisk-genderMale-groupControl
Class siteMelbourne-numRiskNoRisk-genderFemale-groupControl
Class siteMelbourne-numRiskanyRisk-genderMale-groupCase
Class siteMelbourne-numRiskanyRisk-genderFemale-groupCase
Class siteMelbourne-numRiskanyRisk-genderMale-groupControl
Class siteMelbourne-numRiskanyRisk-genderFemale-groupControl
Class siteNewcastle-numRiskNoRisk-genderMale-groupCase
Class siteNewcastle-numRiskNoRisk-genderFemale-groupCase
Class siteNewcastle-numRiskNoRisk-genderMale-groupControl
Class siteNewcastle-numRiskNoRisk-genderFemale-groupControl
Class siteNewcastle-numRiskanyRisk-genderMale-groupCase
Class siteNewcastle-numRiskanyRisk-genderFemale-groupCase
Class siteNewcastle-numRiskanyRisk-genderMale-groupControl
Class siteNewcastle-numRiskanyRisk-genderFemale-groupControl
Class sitePerth-numRiskNoRisk-genderMale-groupCase
Class sitePerth-numRiskNoRisk-genderFemale-groupCase
Class sitePerth-numRiskNoRisk-genderMale-groupControl
Class sitePerth-numRiskNoRisk-genderFemale-groupControl
Class sitePerth-numRiskanyRisk-genderMale-groupCase
Class sitePerth-numRiskanyRisk-genderFemale-groupCase
Class sitePerth-numRiskanyRisk-genderMale-groupControl
Class sitePerth-numRiskanyRisk-genderFemale-groupControl
Class siteSydney-numRiskNoRisk-genderMale-groupCase
Class siteSydney-numRiskNoRisk-genderFemale-groupCase
Class siteSydney-numRiskNoRisk-genderMale-groupControl
Class siteSydney-numRiskNoRisk-genderFemale-groupControl
Class siteSydney-numRiskanyRisk-genderMale-groupCase
Class siteSydney-numRiskanyRisk-genderFemale-groupCase
Class siteSydney-numRiskanyRisk-genderMale-groupControl
Class siteSydney-numRiskanyRisk-genderFemale-groupControl
Variables age
Input 100105SA sitePerth-anyRiskAnyRisk-genderMale-groupCase 23
...
As the number of categorical variables really complicates the
specification of contrast vectors, I was wondering if you could confirm
whether these vectors are correct:
Main effect for haplotype (Risk vs No Risk):
0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5
-0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5
0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5
-0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Main effect for gender (Male vs Female):
0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5
0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5
0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5 0.5 -0.5
0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0
Main effect for group (Case vs Control):
0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5
0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5
0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5
0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0
Interaction between gender & group:
0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5
0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5
0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5
0.5 -0.5 -0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0
Interaction between gender & haplotype:
0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5
-0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5
0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5
-0.5 0.5 -0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0
Interaction between group & haplotype:
0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5
-0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5
-0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5
0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Interaction between gender, group, & haplotype:
0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5
-0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5
0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5
-0.5 0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
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