Dear all,
If you have downloaded the development version of FreeSurfer any time during the last 3 weeks, you may have experienced problems with the modules that segment the hippocampal subfields, nuclei of the amygdala, and substructures of the brainstem.
This is due to a very small bug that we will sort out immediately; I expect it to be fixed in tonight’s build.
However, if you have downloaded the development version during these 3 weeks, you don’t need to download the whole thing again. You can simply edit the following two files: $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt $FREESURFER_HOME/average/BrainstemSS/atlas/compressionLookupTable.txt and replace “Left-Thalamus” by “Left-Thalamus-Proper”.
Apologies for the inconvenience,
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com