‘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.

Best Regards,
Jeffrey Neal
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.edu> wrote: