Hello Freesurfer Experts,
  

I wanted to see if I am setting up qdec correctly.  I am using cortical thickness as my measure.  When using the Qdec gui in Freesurfer 6.0 i supplied the following files:

qdec.table.dat which contains the following:
Subject Group Gender Age Site Yrs_Education


For categorical variables I created the following
Group.levels
HC
PAT

Gender.levels
Male
Female

Site.levels
1
5
6


For continuous variables such as Age and Years of Education here is a significant difference between both groups.


1) Should I demean age and Years of Education before creating the table?  The tutorial uses the actual values (70 73 etc) but a previous user post said that we should deman the values for covariates.  What is the preferred method for the qdec gui?

2) For nuisance variables in the design matrix I selected both age and years of education.  For Discrete fixed factors, I only selected group as this is the independent variables I was interested in.  For categorical nuisance variables such as Gender and Site, are these ignored by the model if they are not highlighted?  Although they are not my independent variable are they accounted somehow if they are not highlighted as the independent variable?  They do not appear in my nuissance variable box so I guess I am not sure if they are used in the model or not. 


3) The dods / doss options are missing from the Qdec gui from Freesurfer v6.0.  Which is the default used in this case?  Is there a way I can change this?

Thanks,
Ajay

On Thu, Apr 21, 2016 at 9:15 AM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote:
Hi Freesurfer Experts,

I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii) to perform a cortical thickness analysis. I used qdec with a surface-based morphometric analysis to compare two groups. As my discrete fixed factor I used group membership.  As Nuisance factors I used age (years), sex (0/1), site(1-10) and years of education(years).  I used Threshold min=2, max=5 which I assume refers to a T-stat threshold.  I see an FDR correction which and the Monte Carlo Null-Z simulation.

1) Do I run both monte carlo and fdr or just one after my figure apprears?
Is the monte-carlo with threshold = 1.3(0.5) similar to a clusterwise threshold with a fixed p value? 
Are results valid when just setting the threshold min=2, max=5 but they are just uncorrected results?


2) When running Qdec with no nusiance factors and just a discrete fixed factor of group membership, my results look almost identical to AFNI's 3dttest++ output when the tmin=2.  However, when I add the nuisance factors the results between the two softare packages are different. 

When nuisances covariates are added does Qdec still use a ttest or switch to some other method? 


How is centering assumed between groups for covariances? Is the mean from each covariate calculated and removed from each group separately based on group membership or calculated together with all subjects and removed?

Does the analysis assume to have pooled or unpooled variance across the two groups?


3) For the viewer it displaces a logarithmic scale  from what I have read in other papers.  Is there a way to switch this to displace tvalue?

4) There was a previous post I saw yesterday saying qdec only uses 2 nuisance covariates and so I wanted to see if this is the case or not so I can try to understand why my afni and freesurfer results match with no covariates added but are very different once covariates are added.


Thanks,
Ajay