In group analysis, I have found a large cluster of voxels (for cluster-defining threshold, say, P < 0.001) that spans multiple regions of interest under a given atlas (say CA_N27_ML without loss of generality). Running 3dclust can provide information such as coordinates of the peak voxel in the cluster (i.e. highest t-stat or beta).
Is there any AFNI function that directly provides the same information as 3dclust, except breaking it down by region of interest in the cluster? For example, suppose a whereami report indicates that cluster A (consisting of 553 voxels) resides in Right Superior Parietal (59%) and Right Angular Gyrus (41%) per the CA_N27_ML atlas. Can I directly get the same information as 3dclust separately for overlap between cluster A and Right Superior Parietal and the overlap between Cluster A & Right Angular Gyrus?
See the -omask option for whereami. That is also available through the clusterize plugin’s wami button.
Thank you Daniel. I’m familiar with the -omask option. However, is there an existing function to use results of the “omask” option of whereami in breaking down 3dclust output (peak voxel, center of mass coordinates, etc) for each cluster? I suppose this might be overkill in terms of reporting results since mapping between significant clusters and ROIs on any atlas are ultimately approximations to begin with.
You can choose whichever set of coordinates you like - either center of mass or peak coordinates of the clusters. If you have the list of coordinates either from the Clusterize plugin or 3dclust, you can feed those coordinates into whereami as in this example taken from afni11_roi.pdf in our class handouts:
3dclust -dxyz=1 -1clip 99.0 1 200 func_FullF+tlrc > clusts.1D
whereami -coord_file clusts.1D’[1,2,3]’ -tab