Dear FreeSurfer Developers,

I think my earlier email may have gotten lost. 

I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0:

longHippoSubfieldsT1.sh PAWS001_base_FS 

I received no errors and everything seems to have run fine. But on computing the subfields using the following command:

quantifyHippocampalSubfields.sh T1.long PAWS_longitudinalhipsubfields.txt

I noticed that all of subfields have negative volume values. I checked the individual text files within each subject's timepoint and indeed the output is showing negative volumes.

I have also tested the same subject and run the cross-sectional hippocampal subfield pipeline using the following command:

recon-all -s PAWS001_TP1_FS -hippocampal-subfields-T1

I'm really not sure why the longitudinal pipeline is showing negative values. Could it be a Freesurfer version issue? Am I doing something wrong? It is especially mind-boggling since I receive no error and the command is running smoothly! Please help. I have attached the text files of the same subject run cross-sectionally and longitudinally.

 1.  A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt
  2.  The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt

Thank you so much!!

Best regards,

Ashwati