External Email - Use Caution
Looks like python3 tries to write/process a string into a file when running the res-config script and fails to translate something to a utf-8 character. If your locale says you are using UTF-8, e.g., $ locale LANG="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_CTYPE="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_ALL=
- then it should work to use this grep command to find files with non-UTF8 characters in them, e.g. $ grep -axvq '.*’ file.txt The -q will prevent displaying the non-utf8 characters which might screw up your terminal session. This thread gives some examples of when that error occurs and how to unmangle the string,https://secure-web.cisco.com/1K3cgYD2bSzKyvPVJ_FeWPCrJhQSWfAKprwIwga7NpojJpm... - R.
On Mar 27, 2023, at 22:14, David Lau <drlauci@gmail.com> wrote: External Email - Use Caution Hi,I tried to run Freesurfer (macOS-7.1.1) to the command line and the terminal replied, "DavidLaus-MacBook-Air:local davidlau$ recon-all -i /Users/davidlau/Desktop/testing/1RAS.nii -subject /Users/davidlau/Desktop/testing/$d doneTraceback (most recent call last): File "/Users/davidlau/Documents/freesurfer/python/scripts/rca-config", line 143, in <module> file.write(arg + '\n')UnicodeEncodeError: 'utf-8' codec can't encode character '\udcc3' in position 0: surrogates not allowedERROR: could not configure recon-all parameters"A similar question has been retrieved from the mail list (20 Jul 2020) by Molly and Andrew replied that there might be a non-unicode character accidentlly passed to the command line and recommended manually typing out the recon-all command. I've tried this several times but the same error message popped out. Any suggestions would be much appreciated.David_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer