I can add that running the -hippo-subfields flag separately did work:

recon-all -s SUBJECTIDENTIFIER -hippo-subfields

Is there a reason the order of processing should matter? Is there a way I can change my recon-all call (below) so that hippo-subfields will get processed (so I do not have to make a separate call)?

recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all

Thank you,

Sal

On Sun, May 26, 2013 at 2:33 PM, Salil Soman <salsoman@stanford.edu> wrote:

Dear Freesurfer Experts,

I have been running freesurfer 5.3 without any reported errors using the following command:

recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all

However, when I look for any of the hippocampal subfield stats (as described on http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do not find any of them.

Any suggestions on what I am doing incorrectly?

Best wishes,

Salil Soman, MD, MS