Hi, Greg
I use to process my subjects with:

recon-all -s subjid -all -hippo-subfields

The -all flag makes the program run all the 3 stages (autorecon1, autorecon2 and autorecon3) in sequence. Only after this it starts the hippo-subfields stage. If you do not have any special reason to run each autorecon in a different line in your script I suggest you just use the -all flag. But if you need to separate each stage you can use:

recon-all -s subjid -autorecon1
recon-all -s subjid -autorecon2
recon-all -s subjid -autorecon3 -hippo-subfields

No need to add the hippo-subfields flag for each stage: you would just repeat the same process and waste time. Indeed, if you check https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation you will see that "...the program needs the FreeSurfer-generated files "aseg.mgz", "nu.mgz" and "talairach.xfm"
At least, aseg.mgz will not be available before completing autorecon2. So I guess if you add the hippo-subfields flag after autorecon1 stage it will return an error.

Marcos
Em Qui, 2014-08-07 às 16:05 -0500, Gregory Kirk escreveu: 

we have freesurfer set up on our big condor cluster, i asked that the

-hippo-subfields be added. they have it set up to run in 3 stages
autorecon1 autorecon2 autorecon3 
they added the flag to all 3, i think it would only be needed on autorecon3, but don't think it would
cause harm, just be ignored in the first 2 ?

thanks

greg
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