I am following up on some issues where we see some effects we really don’t expect when analyzing our data with qdec.  They look like they could be some slightly bad data from scan issues, segmentation problems, etc.  This is a large set of scans so I would like to script out a routine to get the thickness values for each vertex in a region, then look for outliers to help us understand if this is real or a problem.

How can I retrieve the thickness values for all of the vertices in a region?   I am using the routine below, but the labels don’t seem to be the same across subjects – apparently I need to understand how the label numbers/lists match with the various surfaces.  What surfaces,  annot files and label numbers would be the appropriate ones to use for this?  Does the rest make sense?

I have been loading the pial surface and using

Labl_import_annotation aparc.annot

Labl_save 30 l_ROI1

Then in matlab something like:

l_thick = read_curv ('$path/$subject/surf/lh.thickness')

l_roiverts = read_label('$subject,'l_ROI1')

nvert1 = size(l_roiverts)

for k = 1:nvert1(1,1)

ind = l_roiverts(k,1)

    l_ROI1Thick(k,1) = l_thick(ind,1);

end

hist(l_ROI1Thick,100)

print -djpeg -f1 -r150 l_ROI1Thick_$subj

Thanks for your time,

Ronald Pierson

Chair of Imaging, PREDICT-HD

Manager, Research and Development

Department of Psychiatry, Carver College of Medicine

W-278 GH, 200 Hawkins Dr

Iowa City, IA 52242