On 8/24/14 8:54 PM, Bronwyn Overs wrote:
Hi Doug,

Thanks for your response. I was able to follow the steps you detailed and have ended up with a .dat file containing a list of values for each subject. Just a couple of follow up questions:

1. In my analysis I was using rh thickness as a dependent measure. So, do the individual values I have generated (using the below command) represent average thickness of the labelled area for each subject?
Yes
2. If I where using area or volume as the dependant measure, how would i generate label specific stats for those measures?
Do you mean you want to run qdec using area or volume to generate a new label or that you want to get area and volume measures for the thickness-based label? If the latter, then run qdec with area/volume as the dependent measure making sure to spec a different output folder. This will create a new y.mgh file. Then run the mri_segstats command on it.
2. Are the generated stats measured in mm2?
For thickness, they will be mm, area mm2, volume mm3.
3. What is the function of the flag "--id 1"?
It just says to generate stats for the label. If you don't include that flag, then it will generate 2 numbers, one for all the vertices in the label, and one for all vertices not in the label
doug

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

On 22/08/2014 3:27 am, Douglas N Greve wrote:
Create a label of the cluster, then run

mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 
--avgwf cluster.dat

where y.mgh is the file created by qdec in the qdec output folder and 
make sure to use the full path to the label. The output will be 
cluster.dat and it will have
have a value for each subject. Does this work for you?

doug


On 08/20/2014 07:36 PM, Bronwyn Overs wrote:

Dear Mailing List,

I have just completed a QDEC (v5.1.0) analysis of the following design:
Measure:    thickness
Smoothing (FWHM):    10
Hemisphere:    lh
2 Discrete (Fixed Factors):    group (2 levels, AtRisk & Control) and 
gene (2 levels, CC & TTorTC)
1 Nuisance Factos:                age

On completion of the analysis, I have selected the following results 
in the display tab: "Does the average thickness, acounting for group, 
differ between CC and TTorTC?". I have then completed an FDR 
correction by clicking the "Set Using FDR" (Rate 0.05) button. The 
following info is then printed to the terminal window:
        MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798
        Found 59 of 163842 vertices above FDR threshold (of 4.74798)
I have then hit "Find Clusters and Goto Max" and found there to be a 
single cluster in the medialorbitofrontal, with a size of 26.09 mm2.

I would now like to know what the mean thickness is for that cluster 
at each level of my gene variable. How can this information be obtained?

-- 

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

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