External Email - Use Caution
If you edit the file $FREESURFER_HOME/FreeSurferEnv.csh such that line 183 does not contain the semicolon between the “if” and “then” in your MacOS freesurfer installation, that should eliminate the error you listed before the job was killed. So you could try running your recon-all again on MacOS (and do not run anything else on the machine during recon-all, e.g., browsers, videos or anything that would consume additional memory). - R.
External Email - Use Caution
Thanks for the suggestion. However, after changing the FreeSurferEnv.csh line 183, which now looks like this:
"else if ( -e $HOME/fsl) then"
- I am getting the same error: „Running SynthStrip model version 1
Input image read from: /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon/NVR-1/mri/orig.mgz
Processing frame (of 1): 1 Killed“
No other program was running during the test.
Running synth trip alone led to:
(base) MBP-von-Lukas:~ lukasdiedrich$ mri_synthstrip -h
usage: mri_synthstrip [-h] -i FILE [-o FILE] [-m FILE] [-d FILE] [-g]
[-b BORDER] [-t THREADS] [--no-csf] [--model FILE]
Robust, universal skull-stripping for brain images of any type.
optional arguments:
-h, --help show this help message and exit
-i FILE, --image FILE
input image to skullstrip
-o FILE, --out FILE save stripped image to file
-m FILE, --mask FILE save binary brain mask to file
-d FILE, --sdt FILE save distance transform to file
-g, --gpu use the GPU
-b BORDER, --border BORDER
mask border threshold in mm, defaults to 1
-t THREADS, --threads THREADS
PyTorch CPU threads, PyTorch default if unset
--no-csf exclude CSF from brain border
--model FILE alternative model weights
If you use SynthStrip in your analysis, please cite:
----------------------------------------------------
SynthStrip: Skull-Stripping for Any Brain Image
A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann
NeuroImage 206 (2022), 119474
https://secure-web.cisco.com/1DYYVAUIeA7ALFZxkYrccwu5c-GrmouPW82wBhc9ne5R04o...
Website: https://secure-web.cisco.com/1EAUMGmC_HMWw3Qxxks83mikqcTaLkYAd9pEJuytKQuJPJd...
I hope you have further suggestions.
Best, Lukas
Am 15.09.2025 um 05:41 schrieb fsbuild fsbuild@contbay.com:
External Email - Use Caution
If you edit the file $FREESURFER_HOME/FreeSurferEnv.csh such that line 183 does not contain the semicolon between the “if” and “then” in your MacOS freesurfer installation, that should eliminate the error you listed before the job was killed. So you could try running your recon-all again on MacOS (and do not run anything else on the machine during recon-all, e.g., browsers, videos or anything that would consume additional memory).
- R.
_______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1MBGNRMdGHxeJmnK2f6uUbhUM4Bp2XE3zc3uZ3ZJ800I5aB... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1aOqY4frO8pQElcuwjxjN6fB6i8eAVhHb1LUj3Uu5fNlJ4U... https://secure-web.cisco.com/1aOqY4frO8pQElcuwjxjN6fB6i8eAVhHb1LUj3Uu5fNlJ4U0VLj2bKo6e4UyIJKKztDlcn4IFZes1wI8YaCtJanwJvKkdsKO0wY_v2oteObLC_9YvbXPYRsRciHrKkXFrv0DqSqLvPHtXNe63uTyb8qn8LoKZAlM20dWEeZlIpB0U449foD75FgJQQ5YknyZ6xOWGH1MpdtuON1NRpsU45oSxRTULgl1qLWeB621sIY0Et7DigED2WaXuWvUx2ORZqHW9NkI2AW-GkOxNB9B8oV7R19jrwOGaSGOTR8SQsAxZmXe1kDYFJnuzEzSGkKUjvyqihJ2rCS29XpxteQ6EIQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Diedrich, Lukas -
fsbuild