Martin,

To answer question 1, the fsaverage surface is used as a target surface to which the data (ie thickness) of each subject in the group is sampled and then smoothed, so the accuracy of the recon of the fsaverage subject itself is not relevant to accuracy of the group analysis.

For 2., unfortunately, the only way to get qdec to recognize ?h.pial_lgi is via the 'hack' that you mention: renaming the files as 'thickness'. A feature to be added to qdec is the reading of a text configuration file to allow selection of arbitrary surface data files into the qdec menu. Actually, I think I might implement that feature this week, as I hate that hack, and can post this version of qdec for you if you want.

To create the smoothed ?h.pial_lgi files, you would do this:

recon-all -s subjid -qcache -measure pial_lgi

and it will create the fsaverage sampled and smoothed data for each subject.

For 3., I think you are in new territory here, the first to do this, so you will have to experiment. Although 0mm smoothing, as you suggest, seems reasonable.

Nick

On Sun, 2008-10-26 at 21:41 +0100, Martin Kavec wrote:

Hello all,

I have started with a group analysis using qdec and have some questions:

1. loading fsaverage into tkmedit along with rh.white and lh.white surprised

me that the pial surfaces do not run under the skull, as I see it on a single subject but copy the white matter. It is also correct, but it looks a bit odd. I suppose that this is a result of averaged out WM, but my concern is whether it can anyhow affect the analysis

2. I am interested in group analysis of LGI. I do not see however ?h.pial_lgi

in fsaverage. Also when I run qdec, lgi is not among the parameters available for testing. I could backup say the thickness files and than rename my lgi results as thickness, but if there is a more straightforward solution I would like to avoid this trouble

3. Since lgi is for each vertex calculated over a certain diameter, thus has

inherent smoothing. Therefore I would tend to use 0 smoothing in GLM. What do you think about this idea?

Thanks,

Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer