Creating the Flatmaps

Create the Flatmap

FreeSurfer's Guide to Cutting the Final Surface

• • In the past, we have used the retinotopy data to help with the calcarine cut, to try to cut dorsal and ventral V1 cleanly (at the horizontal meridian representation).  However, this is unnecessarily complicated as it usually requires making the cut a couple of times to get it right.  It is better to draw ROIs on the inflated surface so that you don't skip nodes that are lost during the cutting process.  Additionally, we now defined V1 as a single ROIs by default, not split by ventral-dorsal.  Besides, if you go down the center of the calcarine, you should be very close to the horizontal meridian representation anyway.

  • For the calcarine cut, it can still be useful to look at eccentricity data to see how far you should go - ideally, make the cut so that you are just shy of the foveal representation.  But again, this is all for display purposes only so that you can see the entire cortex in one view.  None of this should affect any analysis.

  • Note that we have not typically created the "Occiput Surface".  If you decide you want this for display purposes later, you can always create it then.  You'll just have to update your SUMA directory, potentially by hand so you don't overwrite important files people have placed there.

Steps For Creating the Flatmaps 

1. mris_flatten -w 0 -distances 12 7 -p 15 rh.full.patch.3d rh.full.patch.flat 

   • Change highlighted portions to lh when necessary

   • Go here for help with the function mris_flatten

Next Steps

       Make sure to check the new maps for errors or artifacts. 

       The original steps from the KLab can be found in the link below.