On 8/19/16 5:21 PM, Gold, Andrea (NIH/NIMH) [F] wrote:

Hi,

I’m trying to extract the average thickness per subject in significant clusters from a Qdec analysis, and hope to clarify 2 things re: the “cache.th13.abs.y.ocn.dat“ output from this command: mri_glmfit-sim --glmdir (dir) --cache 1.3 abs --cwp 0.05 —2spaces

I’ve attached all relevant output files.

This analysis has 2 clusters, and I understand the 2 clusters match the order of the clusters in the cache.th13.abs.sig.cluster.summary file (left=cluster 1, right=cluster 2).

1. Would you please confirm whether the rows of the

cache.th13.abs.y.ocn.dat“match the order of subjects listed in the qdec.fsgd file?

Yes, I think so. There should be a y.fsgd file in the output folder, and that will have the actual order used.

2. Also, I noticed the cache.th13.abs.sig.cluster.summary file lists

MNI coordinates – is there a way to get this to print Talairach coordinates from the mri_glmfit-sim command? If not, that’s fine – I can get them from qdec but just curious.

Not from mri_glmfit-sim. But you can look in the log file and pull out the mri_surfcluster command line, remove the --no-fixmni argument, and just re-run it.

Thanks! Andrea

-- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.gold@nih.gov applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov

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