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.
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 -autorecon1
an
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