hi kristofer,
the labels tksurfer uses for the two retinotopic coordinate maps, i.e., the eccentricity and polar angle maps, denote the temporal phase of the activation of each voxel driven by the periodic visual stimulus. depending on your stimulus, these phases computed by the analysis will correspond to different regions of the retinotopic map, so the color map that you see in the display is not absolute. for visualization, you can adjust the default color map from within tksurfer from the "Configure Overlay Display" window (which it looks like you've found) and the "View -> Configure... -> Phase Encoded Data Display..." window.
as for the field sign map, the yellow-blue reversal is probably due to your choice of stimulus polarity, which is specified in the paradigm files. if you prefer having yellow correspond to positive field sign and blue to negative, then simply pick one (not both!) of the retinotopic coordinates, e.g., the eccentricity, and reverse the assigned direction polarity by editing each of the paradigm files. that is, in each paradigm file (named "rtopy.par" by default) within all 'eccen' run directories, change the 'direction' to 'pos' in those that specified 'neg', and to 'neg' from 'pos' in the rest. then repeat the analysis by re-running the "sfa-sess" and "paint-sess" steps.
when you view the results with "surf-sess", not only will you see the field sign maps reversed, but you will also see a change in the color progression in the eccentricity maps.
-jon
On Fri, 15 Sep 2006, kristofer kinsey wrote:
I have a question regarding colour labelling for the retinotopic maps generated by Freesurfer. I'm running Freesurfer-Linux-rh9-stable-pub-v3.0.2 and have successfully generated the polar, eccen, and field sign maps (no errors). The images seem to differentiate the occipital regions, except that the colour labelling appears to be incorrect. In the eccen image, for example, the order of the colours start out as red, green, blue and using the Configure Overlay Display Inverse it's green, blue, red. According to my notes one should see fovea=red, parafoveal=blue and periphery=green. Also, with the field sign image, the area that should be V1 shows up as blue instead of yellow (can't seem to invert the colours).
I've since gone back to double check that my procedure is correct and re-checked my registration and can't seem to find my mistake. I was hoping to get some help to fix this problem. In case it helps, I've attached a few images of the maps that were generated.
Cheers
kk