I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing.
I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in):
tksurfer-sess -a rtopy.self.?h -s sessid
it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code:
tksurfer-sess -a rtopy.self.?h -s sessid -map angle
but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5?
For reference in freesurfer4.5, I would load retinotopy data by using this command:
tksurfer subjname ?h inflated
and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset.
Can you help me figure out how to get my data to display correctly?
Thanks,
Katie