I had a couple questions relating to how to perform retinotopic analysis and view the results in the new Freesurfer 5.0 distribution (bear with me, previous I was using Freesurfer 4.0.2, so there's probably a bunch of changes that are confusing me).
1. I was able to create a new analysis with mkanalysis-sess, and compute the stats with selxavg3-sess. But I'm a bit confused on displaying the data. When I use tksurfer-sess I can see the sig map (which isn't really helpful for determining regions) or use the -map angle command and see something that looks a bit like retintopy but in the heat overlay display type (sorry, not sure the correct terminology here) instead of the standard color wheel. When I try to change the overlay display settings to color wheel and complex it becomes all a single color (green). Perviously I also had to change the phase encoding display settings to 2.0 plus some offset (which I can't actually do right now do to a bug I'm having), but you would at least still see some color differences with the 1.0 phase setting, and I'm not getting any of that. What am I doing wrong?
2. Previously, you could load the brain with tksurfer (not tksurfer-sess) and load data through overlays and loading the real and imag .w files created with paint-sess. I know that now paint-sess isn't needed, but when I try to load the real.nii and imag.nii or even angle.nii this doesn't work. Can you only load retinotopic data through tksurfer-sess command line now?
3. When I try to change the fthresh in the command line, it seems to read it, but then overwrite it with retinotopic data. Is there no way in the command line to change the fthresh value?
4. In the analysis example I was following you had to create a separate analysis for lh and rh, why is this?
thanks!
Katie