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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
