From Functional Activation on Surface
If you are looking at functional activation on the surface and would like to save some active region as an ROI, you can currently do so in tksurfer.
As an example, we will show you how to do this on the FSFAST tutorial data but feel free to use your own. To use the tutorial data, you must do:
setenv SUBJECTS_DIR $TUTORIAL_DATA/fsfast-tutorial.subjects cd $TUTORIAL_DATA/fsfast-functional
If you are not at an organized course, $TUTORIAL_DATA should be set to the path where you downloaded all the tutorial data.
Open a subject using tksurfer-sess:
tksurfer-sess -s sess01 \ -analysis workmem.sm05.lh \ -c encode-v-base \ -c emot.dist-v-base \ -c probe.avg-v-base \ -c emot.dist-v-neut.dist
If you want to play with the threshold, you can do View > Configure > Overlay or use the shortcut and left-click on the Show Overlay button 
on the Tksurfer Tools Window. Make sure to hit the spacebar after you change the Min or Max value in order to see the results.
Click anywhere inside an active region that you want to save as an ROI. Click on the Custom Fill button on the Tksurfer Tools Window. Chose "Up to functional values below threshold". Fill from "Last clicked vertex". And your Action is "Create new label". Now click the Fill button. You should see the region you chose turn white and then back to its orignal color except now it will be outlined in yellow. On the Tools window, go to File > Label > Save Selected Label. A box will open which wants to save the ROI in the subject's label directory.