Question about FSL atlases and ROI segmentation

1

Hello all,

I’m working on creating a standard set of MNI ROI structures for our lab and have a few questions about the way that FSL handles atlases:

  1. Given that the atlas .xml files have each structure label listed, is there a way to loop through an .xml file and extract each labeled structure? Or does one need to use fsleyes or fslview and output them one by one?

  2. Before I work to segment the Harvard Oxford (and others) atlas myself, I was wondering if there is an existing repository of extracted structures in MNI space (e.g., Left Amygdala, Right Putamen, etc. etc.) that lives somewhere in the FSL directory or somewhere else that is open source but I can’t find?

Thank you so much!

Best,
Megan