I am hoping to make a mask of all regions of TT_Daemon for 3dTcorrmap. Because I want to save time in processing and get more specific information on TT regions.
Can I do this mask in whereami? Or I need to put all these regions together using 3dTcat?
The regions are already all together in the atlas dataset. Typically you will find this dataset in the AFNI binary directory named TTatlas+tlrc. This dataset has two volumes, the first (subbrick 0) has gyral areas, and the second (subbrick 1) has the Brodmann areas. There are a number of errors in this atlas despite its long availability and a number of other issues with it too. Incorrect drawing, the lack of a suitable template volume, overlapping of the thin Brodmann areas, coarse slicing - all present a fair amount of difficulties. These issues are discussed in our class material and elsewhere on this messageboard. Still the atlas can be used as a fairly vague guide for regions. Consider the other available atlases and the one supplied with AFNI.