External Email - Use Caution
Thanks for your response. I tried moving the .local directory and rerunning the command but it still gave me the same error despite the fact that I manually corrected all the directories. I attached a screenshot so hopefully the image quality is better.
From: fsbuildmailto:fsbuild@contbay.com Sent: November 15, 2022 10:07 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: Eric Yinmailto:eric.yin@mail.utoronto.ca Subject: Re: [Freesurfer] aparcstats2table segmentation fault error
You don't often get email from fsbuild@contbay.com. Learn why this is importanthttps://secure-web.cisco.com/1lRk6KkAxnHXMoVnv5Yfy7p33mx-_tDw1IO8xyeW-Sc4s2WsE5CIR5wOkEAoipJHfMToVsBCOIzXkR6ueDU-far7wue8zxZ9dXGMmdEIhbP_v0UdSHiu6vvzdkb0wNtE--EEcUFKNEufPcNDV0JzoR24L43466nSyFIhZpOLVio-3KuQ-G9ysIQkUAke4GU6WTSXNiNLLnVhAhuuhKH3THBwYwxCzdmmQBwr1EAszdPM1bHWrsd6TNVfR1PaZr67SI4V3ZEdcz3TrdnhrX06diA6JOq7_K_xu_fTaqYe2EacPmgwugLx0HM7t27Gnx6RnYv3Gwj3koLZrXZRfCq47wA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists. And it looks like you are using a “dot” directory named “.local” in your path for FREESURFER_HOME which is usually reserved for hidden subdirs in the shell. I would not name any subdirectory to begin with a "dot" for normal use with the shell, so try
$ mv .local local
… reset FREESURFER_HOME, source the setup script again, and see if running the command works.
- R.
On Nov 15, 2022, at 19:59, Eric Yin eric.yin@mail.utoronto.ca wrote:
External Email - Use Caution
Hello!
I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem.
<9ECE8F5D2E7645A5962B55E842687C47.png>
I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core).
<4E289904EB384B21861CA9E16B7DD234.png>
Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6.
<64B17BE84D1E4AFBBF7FFCE28ED15CD7.png>
Please let me know if I’m doing something wrong, or if anyone has run into a similar issue.
Thank you for your time. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ma3sGa-roikw6O7OPuyFfTb9UWXoXXtWq-D_vs8Q7hLzyS...
