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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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