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 pipeline
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
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
descri