Thank you for your advice, Bob. Unfortunately, I can't apply the command you've suggested because my masks lie in separate folders (they are not in the subject directories and I can't really move things around...I am working with a large external hard drive containing a bunch of different people's data. It was given to me as is and it's not very well organized.) Furthermore, the masks all have unique names, and there are 4 different mask sizes for about the 12 ROIs I am investigating. I don't know how to go about creating a script or finding a way to automate doing these commands for multiple subjects, so I'm just doing them individually for now. I am trying to find help locally. Please allow me to give you some idea of how I'm working through this. I'll demonstrate what I'm doing as I'm executing this command for a single subject, and maybe you can advise me how to be able to apply this to multiple subjects.
The masks are located here:
Masks / Data / individual folders for all subjects (all folders have unique names) / afni files (multiple masks for all ROIs)
In the command terminal, I enter one of the subject folders, like so:
cd ../Data/Subj4/
So, I'm in the subject's folder now (where the masks are located, not where the subject's original/clean afni files are. Those are in another directory that I will be accessing, as I demonstrate below.) Every mask for every ROI is in here, but I'm just applying a single, particular mask (e.g. Ir10_t0) to a single, particular ROI (e.g. L_FFA.) So, the command looks like this:
3dROIstats -1DRformat -quiet -mask *unique mask file* /*path to original file within a subject directory* > *path to original file within a subject directory/***.1D
Again, forgive me if this seems trivial or if I've been unclear. Can you suggest a solution? For simplicity's sake, I'd like to execute this 1D output command, just taking 1 mask (Ir10_t0) and 1 ROI (L_FFA), and run it simultaneously for all subjects in a directory.
