help > loading freesurfer results
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Dec 18, 2018  03:12 AM | Jonatan Ottino - University of Barcelona
loading freesurfer results
Hello everyone,

I'm struggling to make a figure with freesurfer's cortical thickness results, but I'm not able to do it properly.

Every time I open Surf Ice and load the mc-z... .annot file (significant results after MC correction), the whole surface turns black (please see attached).

Is there any script or something to do this? 

I already tried to change the parameters manually from the Surf Ice interface, but I failed. I also would like to change the results map color, because the original one (cyan) is hard to discern from the pial's surface background in gray.

Thanks in advance! great tool!
Dec 18, 2018  04:12 AM | Chris Rorden
RE: loading freesurfer results
When you open a map with the ".curv' extension, Surfice assumes you are loading a FreeSurfer Curvature file. That is why it has selected one of the FreeSurfer survature color schemes (which is attempting to darken creases). You can fix this by clicking on the overlay "color" drop down menu and choosing a different color scheme (for example "Red-Yellow"). You might want to check how this file got created - Surfice expects filenames to include the term ".thickness." if they use FreeSurfaces curvature format but represent cortical thickness rather than cortical curvature. Finally, you may want to update to a recent release.