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 <salso...@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 > >
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