External Email - Use Caution
Please keep in mind that the system python installed on both CentOS6 and
CentOS7 (/usr/bin/python) is python 2.X, so scripts aren’t expecting to run a
version 3 via the “python” interpreter found in a standard system PATH.
As far as I know only 1 python interpreter can be returned thru PATH
(whichever python it finds first according to the order of the entries in
PATH).
But you can alias python to be something different in your shell, e.g., here
using csh,
% alias python python3… or alias to whatever python rev 3 you want to run.
If your PATH is set to return system 2.X version, e.g., /usr/bin/python., then
any script like slicedeleay should still find /usr/bin/python thru PATH.
But typing python at the terminal will run whatever the alias points to.
The which command will show you this (CentOS7),
% which python/usr/bin/python% python --versionPython 2.7.5% alias python
python3% python --versionPython 3..6.8% which pythonpython:
aliased to python3% /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE:
slicedelay --help --o slicedelayfile --nslices nslices :
total number of slices in the volume --order order
(up,down,odd,even,siemens) --ngroups ngroups (number of slice groups
for SMS)< … rest of output deleted …>% unalias python% which
python/usr/bin/python
- R.
On Oct 29, 2020, at 21:46, Peled, Noam <npe...@mgh.harvard.edu>
wrote:Thanks!I’m only working with python3, so I prefer to set python to call
python3 and not python2.Is there an option to set the python bin file name used
by FreeSurfer (/usr/bin/python2.7 for
example)? Thanks,Noam From: fsbuild
<fsbu...@contbay.com> Sent: Thursday, October 29, 2020 9:33
PMTo: freesur...@nmr.mgh.harvard.eduCc: Peled, Noam
<npe...@mgh.harvard.edu>Subject: Re: [Freesurfer] preproc-sess error
with FreeSurfer
7.1 External Email - Use
Caution Hello Noam, The
python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run
with a version of python that is 2.X, i.e., $ file
/usr/local/freesurfer/dev/bin/slicedelay/usr/local/freesurfer/dev/bin/slicedelay:
Python script, ASCII text executable$ which python2/bin/python2$ python2
/usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay
--help --o slicedelayfile --nslices nslices : total
number of slices in the volume --order order
(up,down,odd,even,siemens) --ngroups ngroups (number of slice groups
for SMS) Creates an FSL custom slice delay file for use with slicetimer
(--tcustom=sdfile).It has a single column of values, one for each slice. Each
value is the slice delaymeasured as a fraction of the TR and range from +0.5
(beginning of the TR) to -0.5 (end of the TR). Used for slice-time
correction of fMRI. $ which
python3/space/freesurfer/python/linux/bin/python3$ python3
/usr/local/freesurfer/dev/bin/slicedelay --help File
"/usr/local/freesurfer/dev/bin/slicedelay", line 9 print
"USAGE: slicedelay --help";
^SyntaxError: Missing parentheses in call to 'print'. Did you mean
print("USAGE: slicedelay --help")?So I think that means that for you,$ which
python- is going to return a python from your PATH such that typing the command
“python —version” will report it is rev 3.X and not 2.X. You can try
setting the PATH environment variable such that the first python program found
in PATH reports it is version 2.X. - R.On Oct 29, 2020, at 20:47, Peled,
Noam <npe...@mgh.harvard.edu>
wrote: /usr/local/freesurfer/dev/bin/slicedelay_______________________________________________Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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