‘recon-all’ is a shell script that is ready to be run. I don’t understand why they need to have makefile to make recon-all.
Here are the steps to setup Freesurfer environment and run ‘recon-all’:
1. Source the correct Freesurfer environment needs to be sourced before running recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux 2. Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permission 3. Run recon-all https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
(ex. recon-all -all -s <> -i <>)
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jeffrey Neal Sent: Monday, November 11, 2024 10:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Noah Reardon nreardon@umich.edu Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9
Hello,
Thanks for the helpful links. I did double check through everything and it all looks correct; Sorry about the log file I needed to change permissions on it. Here is the log file from the first email and here is an additional one from today as well as some screenshots: After running it once and getting the “terminated by signal 9” error when I try to run it again packages have disappeared out of the freesurfer/bin causing more issues. The command they are running is make recon-all -k. If you need to see the makefile or other things let me know and I will get them for you.
[cid:image001.jpg@01DB3439.51793600] [cid:image002.png@01DB3439.51793600] Best Regards, Jeffrey Neal jsneal@umich.edumailto:jsneal@umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan
On Nov 6, 2024, at 4:27 PM, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote:
