The "u" in the whereami output is meant to show that the region is not identified as left or right. The ctx is Freesurfer's notation for cortex. "lh" is left-hemisphere. Likewise, the G and S stand for gyral and sulcal regions, respectively.

The probabilistic maps are a bit more difficult to work with, but they do allow for a specific region to include a larger number of voxels. You may use a threshold you believe to be appropriate, so if you think a 30% probability threshold is good choice, you can threshold that using a 3dcalc command, for instance, to 0.3. The MPM atlas uses a 5% minimum threshold and assigns the region with the maximum probability above that. That is a different way to use an atlas region that does not permit overlapping regions.

For atlases that are in MNI space, you may want to transform the atlas, rather than your group results, to the space of the template. You can do that with the adwarp command (follow the link in my previous response). Be sure to use nearest neighbor interpolation for atlas regions. Probabilistic region could be transformed with linear or cubic interpolation and thresholded in the TT_N27 space.



Edited 1 time(s). Last edit at 03/05/2018 12:02PM by Daniel Glen.