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
Hi Greg, I would suggest that you only do it with either autorecon2 or autorecon3. With autorecon1, it will fail because it won't find aseg.mgz. You should still be able to run autorecon2 after this mistake, but I wouldn't do it (why let the software exit with an error without need?). If you do it both with both autorecon2 and autorecon3, I believe that the code will be run twice. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
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----- Original Message ----- From: "Gregory Kirk" gkirk@wisc.edu To: "free" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 7, 2014 5:05:27 PM Subject: [Freesurfer] -hippo-subfields
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
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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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Marcos Martins da Silva