Hi Efrat, To look for aseg outliers you'll need to generate a aseg lookup table based on all the subjects in your dataset (-gen-asegLUT). Additionally, in the current version some of the labels the script uses are old and no longer appear in the aseg generated by recon-all, so they will be 0 +/- 0. Sorry for the confusion, we are in the process of revamping this tool to make it easier to use and interpret. -Louis

On Mon, 7 Jan 2013, Efrat Kliper wrote:

Dear FreeSurfer expert,

I am using Freesurfer version 5.1.0. After I run the QA Tool and check my data, I am getting 39 outliers or more for each subject. When I look at the AsegMeans and DefaultAsegMeans files in the QATool library, i see that the mean values in these file for each anatomical label are 0s. Is that OK? what files are you checking for outliers against? My results are in agreement with the literature and i believe non of them should be outliers.

Any suggestion what might be the problem?   Thank you in advance, Efrat