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Apart from the output about the if statement, it looks like your recon-all command did run and then was killed because mri_synthstrip used too many system resources.   That is unless the command took no time to run and immediately exited.     If the command exited immediately after you entered it on the terminal, then the output about the if statement could indicate there is something not right with your recon-all arguments.

Check you can run mri_synthstrip command directly.  A command with actual arguments and processing to do would be a better test, but at least try,

$ mri_synthstrip -h

You could try reverting recon-all to the old behavior where it will not run the newer mri_* commands as part pf the recon-all pipeline by setting the environment variable FS_V8_XOPTS=0.    That should reduce the chances the system will kill the process because of heavy resource usage.

$ export FS_V8_XOPTS=0 && recon-all -s NVR-1 -sd /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon -i /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/5_t1_tfl3d_sag_ti1090_fa9_tr2700_09mm_p2.nii.gz -T2 /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/6_t2_space_sag_081x081x09mm_p2.nii.gz -T2pial -all

- R.

On Sep 9, 2025, at 08:47, Diedrich, Lukas <lukas.diedrich@med.uni-goettingen.de> wrote:

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Thank you for this suggestion. However, changing the shell from zsh to bash did not help as I get the same error.
Any other idea?

Best wishes and thanks for your help
Lukas

Dr. rer. nat. Lukas Diedrich
Postdoctoral researcher
Non-invasive Brain Stimulation (NBS) Lab
Department of Neurology
University Medical Center Göttingen, Germany

+49 551 39 64838 | lukas.diedrich@med.uni-goettingen.de 

<NBS_Logo_klein.png>

Am 05.09.2025 um 22:35 schrieb fsbuild <fsbuild@contbay.com>:

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If you have not already done so, please try running your commands in the bash shell as shown in the page referenced via the below link (scroll down to MACOS).  So far I've seen no issues running various recon-all tests with 8.0.0 and 8.1.0 on a MacMini running Sequoia 15.5 with an M2 processor and 32GB of RAM using the setups listed on that page.
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads/rel8notes

- R.

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