Hello gurus (especially Ziad and Paul T):

I have FreeSurfer parcellations and segmentations and a hand-drawn mask (at different resolutions) that I wish to bring into 3dNetCorr, but I only want to use some of the parcellations and segmentations because my 7T EPI has a smallish FOV. Two questions:

I assume I need to get these two files into the same resolution before further processing, right? Should I resample them into the resolution of the FS ROIs (1mm), the hand-drawn mask (0.7mm) or the EPI (1.4mm)? I'm thinking the last one.

I see I can use the -mask option to deal with the FOV option but the FOV will only allow a sliver of some of the parcellations to have their timeseries pulled... how do I specify which ROIs to actually use? I'm unclear if -in_rois can take a .txt file and if so what the formatting should be.

THANKS

-Sam Torrisi

Section on the Neurobiology of Fear and Anxiety
National Institute of Mental Health