Hi Doug,

Many thanks for the valuable answer and help.

I would appreciate a lot if you can advise me how I can get in a table from QDEC the clusters after I find the clusters and also the mean value for the cortical thickness within this clusters. I know in GLM the files are coming as an output but I cannot see in QDEC this files. The same question for the values after running FDR in QDEC.

My last question is what should I do if for one case I get error when I do FDR and thresh is becoming 3.18 (instead of 2) and QDEC cannot run the statistics for the clusters. Also it is possible to get more clusters after running FDR in comparison with the no. of clusters when I set up the thresh 2?

Thank you very much and have a great weekend! Antonella

________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 22, 2011 3:53 PM Subject: Re: [Freesurfer] Contrast Vector while eliminating age and gender

If you want to "eliminate" age and gender, you have to include them in the model. In this case, they are called "nuisance" regressors. But this is just an arbitrary name. The model is constructed of regressors, some of which you care about and some you don't, but the GLM is run in the same way regardless. Where the difference comes is when you go to construct contrast vectors. If you want to treat some regressors as nuisance, then put a 0 in their column in the contrast vector. doug

Antonella Kis wrote:

Hi Doug,

Yes, I looked online but in all the examples I found age was included in the study. The same thing for qdec all the examples I saw online are related to a study (a comparison between two groups) but considering age.

I couldn't find any documentation for a study between two groups while eliminating age and gender.

Please advise and sorry for all this questions. Regards, Antonella

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*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, September 22, 2011 12:03 PM *Subject:* Re: [Freesurfer] Contrast Vector while eliminating age and gender

Have you looked at the FSGD examples on the wiki? Do a search for FSGD. doug

Antonella Kis wrote:

...

Dear All,

What should be my contrast vector if I want to do a direct comparison between groups (patients vs. controls) after eliminating gender and age? Should this be [1 -1]?

Should I change my FSGD in

order to be able to compare between

...

patients and controls accounting for age (I want to make sure that the age does not confound my results). Please see attached my FSGD file.

Also, my question is how the clusters are created: the clusters formation is due to a  similar value within cortical thickness(cortical thickness with similar values from patients and controls are grouped together in a cluster (e.g. cluster no.1) while other cortical thickness values are forming different clusters) or the clusters are formed based on age -age grouping (each subject belong to an age cluster)?

Thank you, AK

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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