External Email - Use Caution It reads like something is not right with your setup/shell environment. Once you have setup the freesurfer environment via, e.g., $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetupFreesurfer.sh-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7..4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni FSL_DIR /usr/pubsw/packages/fsl/current
- then the head or start of your PATH has on purpose been modified to contain paths pointing to binaries in the freesurfer tree, $ echo $PATH | tr -s ':' '\n'/usr/local/freesurfer/7.4..1/bin /usr/local/freesurfer/7.4.1/fsfast/bin /usr/local/freesurfer/7..4.1/tktools /usr/local/freesurfer/7.4.1/mni/bin…. rest of output deleted … All python scripts in the freesurfer distribution are automatically run with fspython - which in turn runs the python distribution included in freesurfer. Any, e.g., system, python3 otherwise found in your path should not be used. We do not recommend activating a conda environment, or other python (virtual) environment that will change PATH or set PYTHONPATH after setting up the freesurfer environment. $ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ which python3 /usr/bin/python3 <--- not used by freesurfer$ echo $PYTHONPATH… no output ... - R. Subject:[Freesurfer] HelpDate: Wed, 22 Nov 2023 08:44:18 -0500From: Xincen Wu <xlw...@groton.org>Reply-To:Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>To: Freesurfer@nmr.mgh.harvard.edu External Email - Use Caution Hi,I am using freesurfer. I have gone through with the installation and diagnostics and everything works fine. FOr example, using the command recon-all --help in terminal yields a bunch of directions. Yet, when I enter something like: recon-all -s bert -autorecon1an error pops up saying my python3 is problematic. However, I regularly use python3 and redownloaded it after. Please advise on the issue at hand.Thanks,Lucas<Attached Message Part.txt>
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