Hi Mpark-

You have a few options. The main two that come to my mind are:

A) Take the large ROI and divide it into multiple ROIs using at Atlas.

Many ways to do this, but to divide this into the most simple steps: 1) use whereami to create an ROI of an atlas region / Freesurfer segmentation. Repeat this step for Left and Right and any other sub-regions you'd like 2) Use Clusterize / 3dROIMaker / 3dClusterize to create your clusters. 3) Use 3dcalc to multiply your Clusterize map with the anatomical ROI you made in (1). And finally 3) combine your new ROIs into a joint map using either 3dcalc or 3dTstat. You can then use this combined ROI mask with all your regions of interest for extracting values via 3dROIstats or other programs.

B) Use 3dROIMaker with -mask option to take the highest % or number of voxels in the ROIs (created above using whereami) for each atlas region to get a focal point within the ROI of "hottest" voxels. I've found this useful for pulling out localizer activation for use with say rsFMRI data and the Legendary Paul Taylor was kind enough to add it back in 2013/2014.

For either of these steps, you'll likely need to use 3dfractionize to reduce the dimensions / resolution of your ROI dataset to match your functional dataset.

Let me know if you get stuck in those and I can write out more code or even do a blog post.

-Pete



Edited 3 time(s). Last edit at 09/06/2021 08:35PM by Peter Molfese.