I put three scripts here: http://brainmap.wustl.edu/pub/donna/US/UNC/ login pub password download
For the coords, you'll need a different test -- coord anova: http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation:Statistics#Coordinate_Difference_Analysis_of_Variance One of those scripts does that. But first, you'll need to x-flip either the right or left. I propose x-flipping the left to right, resulting in mostly positive values for x. See flip-x.sh. For your depth, you need to make a composite from your depth files, and the gen_distortion.sh script does that for distortion. You'll want to recompute your distortion using something like that, because the order of the mean fiducial and the individual's fiducial is important. The mean is the first argument to the distortion command. Else you end up with mostly negative values, as you apparently did, and as I did when I first recomputed my term12 version 2 distortion metric. Easy mistake to make, but we want to pump up areas -- not shrink them down. Anyway, that script shows how to generate a composite and compute an average. You only need the composite for your depth case, but the latter comes in handy. (The gen_distortion.sh script didn't exist when it first came up the other day. I just needed to do it, so now it does.) Donna On Apr 5, 2012, at 10:17 AM, gangli wrote: > Hi Donna, > > I would like to test the paired difference between left and right hemispheres > on 3D coordinate position and sulcal depth. Please find the uploaded input > files and help me figure out how to do this. > > Thanks a lot. > > Gang > > > My versions of caret_command can read them all, and the coords/metric all > have roughly 164k nodes -- all good. > But I still don't have your command line, or inputs like I'd expect to a > paired t-test, if that's what you're doing. > For each subject, I have a metric that has a column for 3D variability and a > column for areal distortion. I doubt that you want to get a paired difference > between these disparate measures. > What you need, as input to the paired t-test, is a composite metric/shape > with one column per subject. One composite might have left sulcal depth, the > other right, for example. "It doesn't get any more paired than the left and > right hemispheres of a person's brain." --Tom Nichols > But it could be thickness at different timepoints, twins' thickness maps -- > anything you can pair. But the two composite input files should have equal > numbers of columns, and those columns should be paired (i.e., first col of > each file corresponds to one another; second col of each file corresponds to > one another; and so on). > Hope this helps. > On Apr 4, 2012, at 1:02 PM, gangli wrote: > > Hi Donna, > > > > I have uploaded several generated subjects along with metric and shape > > files. Can you please help me figure out how to average and compose the > > shape and metric files? > > > > Thanks a lot. > > > > Gang > > > > Hi Gang, > > Could you provide the full command line and/or output from running the > > script? It might not work in Windows, but on Linux or MacOSX command line > > you would do: > > paired.sh >& paired.log > > Then upload paired.log here: > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > Depending on what information that gives me, I may want to see more > > information, like your mean midthickness, distortion metric, composite > > scalar files, etc. > > Also, it would be helpful if when you reply you keep the prior message > > history in your reply, so that I don't have to go to the archives to remind > > myself of what you have already done. It is easy to get users confused -- > > particularly when I am using this stuff heavily myself. > > Thanks much, > > Donna > > > > On Apr 4, 2012, at 9:07 AM, gangli wrote: > > > I am using caret_distribution_Windows32.v5.65 and the input is *.metric > > > file generated in previous discussion. Thanks. > > > > > > Regards, > > > Gang > > > _______________________________________________ > > > caret-users mailing list > > > caret-users at brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > > caret-users mailing list > > caret-users at brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
