Hi Dahyun,
Unfortunately it looks as if the fslpython inatallation did not
succeed. I would recommend removing the $FSLDIR/fslpython directory,
and re-running the fslpython_install.sh script.
Cheers,
Paul
On 17/01/2019, SUBSCRIBE D. Yi <[log in to unmask]> wrote:
> Dear Experts,
>
> I’m trying to run bedposts on Mac (10.14). Using X11 (updated version).
>
> The command line is used. The process gets killed with the following
> messages:
>
> ——-
> bash-3.2$ bedpostx /Users/myid/Desktop/DYI_dti_raw/v0/bedpostx_test —nf=2
> —fudge=1 --bi=1000 --f0 --ardf0
> subjectdir is /Users/snuhldy3/Desktop/DYI_dti_raw/v0/bedpostx_test
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
>
> ----- Bedpostx Monitor -----
> An error ocurred. Please check file
> /Users/myid/Desktop/DYI_dti_raw/v0/bedpostx_test.bedpostX/logs/bpx_preproc.e19992
> Killed: 9
>
> ————
>
> When I open the log, it reads:
> "Failed to import the site module
> Your PYTHONPATH points to a site-packages dir for Python 2.x but you are
> running Python 3.x!
> PYTHONPATH is currently: "/usr/local/lib/python2.7/site-packages"
> You should `unset PYTHONPATH` to fix this.”
>
> I checked the python version, and python path:
> bash-3.2$ python --version
> Python 3.7.2
> bash-3.2$ python -c "import sys; print(sys.path)"
> ['',
> '/usr/local/Cellar/python/3.7.2/Frameworks/Python.framework/Versions/3.7/lib/python37.zip',
> '/usr/local/Cellar/python/3.7.2/Frameworks/Python.framework/Versions/3.7/lib/python3.7',
> '/usr/local/Cellar/python/3.7.2/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload',
> '/usr/local/lib/python3.7/site-packages']
>
> In case, I also ran “unset PYTHONPATH” just in case. But the same error
> persists and kills the command.
>
> On a side note, fslpython_install.sh appears to have been correctly
> installed as when I checked, it read:
> bash-3.2$ sudo /usr/local/fsl/etc/fslconf/fslpython_install.sh -f $FSLDIR
> Error - /usr/local/fsl/fslpython already exists!
>
> I deeply appreciate the help.
>
> Thank you very much!!
>
> Dahyun
>
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