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Dear Eugenio, 

I noticed what was the problem. I used freesurfer dev version with the following command:

segmentHA_T2.sh 

I tried to export the hippocampal and amygdala results of several subjects with these commands and now everything works fine. 

quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt

quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt


Is there some difference between the segmentHA_T2.sh  that I used and the command of the website? In that case I would like to use the most appropriated. 


recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>


 Thanks in advance. 


Best regards,