Re: [Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

I usually use this little bash script (named myrecon) to process my images. #!/bin/bash mkdir ~/freesurfer/subjects/$1/mri/orig -p cp ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/ recon-all -all -s $1 -cw256 -hippo-subfields -qcache With this script I get the entire -all

Re: [Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

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

[Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields

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