But I do not expect Freesurfer 5.3.0 Intel binaries to run under the Rosetta emulation environment on a silicon Mac.  Even if it does run, since the M5 Mac OS and CPU architecture are different, your floating point results for any subject would likely not match results from any previous runs on an Intel processor.

Before setting up the Freesurfer environment, I would explicitly run the bash shell, 

$ bash

$ export FREESURFER_HOME=/Applications/freesurfer/8.1.0

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

I would then copy any subject data you want to process into a directory like your home ($HOME) where you do not need any special permission to write to (see below).  The idea is to not modify the Freesurfer distribution by placing your own subject data there.

$ cd

… you are now in your home directory denoted by $HOME ...

$ mkdir subjects

$ cd subjects

…. copy in subject data you want to process ..

$ export SUBJECTS_DIR=$HOME/subjects

$ ls $SUBEJCTS_DIR

… you should see your data …

Processing T1 and/or large images may not work on the silicon Mac unless you have at least 32G of physical RAM on the machine..  Even then it may not work because changes to the recon-all pipeline commands include python code which may require more (virtual) RAM than the memory management can handle.   The recon-all log says 22G of RAM are in use and there 1.5G of RAM free.  I’m assuming you are not running any other apps that cache data in RAM, browsers, etc.

A workaround for this is to tell recon-all to revert back to the previous version of some pipeline commands by setting the environment variable FS_V8_XOPTS=0 on the recon-all command line,

$ export FS_V8_XOPTS=0 && recon-all -i T1.nii..gz -s Pt01 -maskbfs -all

The downside to this is the recon-all command will take longer to finish.

Finally, if you continue to run into errors, you could try downloading and installing a current development build from,

Please keep in mind we do not recommend development builds for long term/ongoing work since they may be unstable.

So to summarize ..

1) try using the bash shell to run commands (and set SUBJECTS_DIR differently)

2) see if a recon-all can complete using export FS_V8_XOPTS=0 && recon-all …

3) if the above does not resolve your errors, try a more recent development build

- R.