After the segmentation I obtained the hippocampal segmented file for each hemisphere. Since I want to use them as mask for my functional scans, I wanted to join the the 2 hemisphere files together (otherwise I would obtain a different Multiple comparison computation), but when i tried doing that in FSL (fslmaths) the 2 files were joined but in very different spatial configuration. Is there a way to join the 2 hemisphere file in Freesurfer?
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