I would like to extract VOIs from the Juelich Atlas for use in whole-brain network analysis. I have written a very simple shell script that extracts each ROI on the basis of intensity value (fslmaths ${ROI} -thr-.5 -uthr+.5 ${ROI}_extracted). This works for every ROI, with the exception of six pairs of regions for which each pair shares an intensity value. These region-pairs are:
IntensityV=9: GM Amygdala_centromedial group L AND GM Amygdala laterobasal group L
IntensityV=19: GM Hippocampus entorhinal cortex L AND GM Hippocampus hippocampal-amygdaloid transition area L
IntensityV=37: GM Inferior parietal lobule Pfm L AND GM Inferior parietal lobule Pga L
IntensityV=47: GM Primary somatosensory cortex BA3b L AND GM superior parietal lobule 5M L
IntensityV=54: GM Primary somatosensory cortex BA2 R AND GM Superior parietal lobule 7P R
IntensityV=99: GM Primary motor cortex BA4a L AND WM corticospinal tract L
Is there a command/set of commands I could use to separate these paired regions post-extraction so that I don't have to manually edit them? FSLsplit maybe?
Any help would be much appreciated, and thanks in advance!
Anna
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