Creating a caret overlay for fMRI data

A clearer and better understanding of functional activation  in the brain is a very important factor for comprehension of a neuroimaging paper. Clearer comprehension = more likely to be cited. Although, there are standard overlays in software package like SPM, they are not so appealing. One of the softwares that allows you to overlay your functional data (and other interesting things) onto cool free surfer like surfaces is caret (van essen's lab). There are different ways of overlaying your data on caret surfaces. I'll give a brief tutorial on some of them.

1. The most common and easy way to do this is by using the function overlay Volume to surface. For a detailed description see Craig Bennet's post here. I'll be using caret version 5.65. You will need an  atlas like PALS atlas (link). You can also have a look at the tutorial here (link). The steps are very easy:
a) Open caret (use the shortcut in windows/type caret5 in terminal in linux).
b) Open spec file PALS(full name) -> Select all (or all the surfaces that u want to overlay) -> Create new spec file (make a copy so that u don't change original atlas ) -> Give any name to it (preferably related to ur experiment) -> Load
c) Go to Attributes -> Map Volume(s) to surface(s) -> Select Metric -> Add Volumes from Disk (in Volume Selection) (if u choose .hdr files from SPM Analyse format, it might give u a warning that .img is required for overlay, ignore this if you have .img of the same name as .hdr in the same folder) -> Map to Spec file with Atlas ( or Map to spec file) Choose your file as the spec file that u just created, select the atlas you want it to be in (e.g. SPM5 or FLIRT etc.), you have to choose the file separately for Left and Right hemisphere. Note: If you choose Map to spec file only, you have to select all coordinate files. -> You can save ur metric files in your chosen folder by selecting Data file button. You may leave it default also. -> Choose your algorithm for mapping. Metric enclosing is the most preferred. -> Finish!!

d) Open your spec file that you had mapped your metric data. If you are using caret5 or higher, you might get a pop up that now you can open two files at a time, you can select new spec only to see only the new spec file. -> Select all -> Load.

 e)Click the button D/C (display control) -> In the page selection select Overlay/underlay - surface. -> select Data type as mapped metric file in primary overlay.

f) Thats it !! Be sure to check that u are overlaying left data onto left hemisphere. (You can also use apply metric L-L,R-R matching in metric selection, but its much easier to do this manually ).

In the next post, I'll discuss how to overlay more than one data on to a single surface in caret with multiple colors.