Hi Kaspar,

It doesn't matter where you place the flags in your command line, as long as all of them are there. Also, -s and -subjid are equivalent, so the first two commands would be the same (although the path to your input data is different after the -i flag, and your subject name is different after the -s or -subjid flag).

Best, Lee

On Sat, 10 Oct 2015, Kasper Jessen wrote:

Dear Freesurfer group,

• I have noticed different ways of writing the 'recon-all' commands (see below). What is the difference between these two ways of writing the command? Or is it the same?
  • recon-all -all -s <tpNid> -i path_to_tpN_dcm
  • recon-all -i  <path/anat.nii.gz> -subjid <ID> -all
• Does it matter where you place the 3T flag in the command line? fx
  • recon-all -i  <path/ID/anat.nii.gz> -subjid <ID> -3T -all

Best regards, Kasper Jessen MD, PhD student