Dear Meena, Running the dev version of recon-all is a really bad idea, as your results will not be reliable or reproducible. I would use dev for the hippo/amygdala substructures and then switch back to 6.0. Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Meena M. Makary" meena.magharious@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, 23 December 2019 at 11:55 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] BrainStem & HippoAmyg segmentation

External Email - Use Caution Hi,

I am using Freesurfer stable6_0_0 (/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin) and I used it for all my subjects, so far. Now I would like to do BrainStem and HippocampalSubfieldsAndNucleiOfAmygdala segmentation which needs me to switch to dev versions. Should I switch to the dev version for getting this segmentations only and switch back Version 6 for future reconall or is it okay to switch to the dev version for good? In other words is there any differences in the reconall between the two versions?

Thank you! Meena

-- — Meena M. Makary, Ph.D. Assistant Professor | Cairo Universityhttp://bmes.cufe.edu.eg/ Postdoctoral Fellow | Radiology, Harvard Medical Schoolhttps://connects.catalyst.harvard.edu/Profiles/display/Person/176550 Postdoctoral Fellow | Athinoula A. Martinos Center, MGHhttps://www.nmr.mgh.harvard.edu/user/4550386 Career Development and Mentoring Manager | OHBM Student and Postdoc SIGhttps://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449