help > loading freesurfer results
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Dec 18, 2018 11:12 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!
J
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!
J
Dec 18, 2018 12:12 PM | 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.