Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1 - Freesurfer

30 Oct 2020


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I don't think a script can see/read that shell alias.&nbsp; That’s why it worked in my example for the slicedelay script to run using a python rev 2&nbsp; (which was /usr/bin/python = the *first* python returned when searching PATH) while the alias pointed to a completely different python (python3 found in PATH) to run from the terminal when you type “python”.
You can put a hash bang line at the top of your scripts to specify them to run with a specific python found in PATH, e.g. below, instead of “python3", “python2” or anaconda python as found in your PATH.
- R.
- - - ver.py - - -#!/usr/bin/env python3
import sys
print(sys.version)- - - ver.py - - -
$ ./ver.py3.6.8 (default, Aug&nbsp;&nbsp;7 2019, 17:28:10)&nbsp;
[GCC 4.8.5 20150623 (Red Hat 4.8.5-39)]
On Oct 30, 2020, at 14:42, Peled, Noam &lt;NPELED@mgh.harvard.edu&gt; wrote:Thanks,In my system, I aliased the python command to a local anaconda python3.8.So to be able to use slicedelay, should I first alias python to python2?&nbsp;Thanks,Noam&nbsp;From:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;&nbsp;Sent:&nbsp;Friday, October 30, 2020 2:37 PMTo:&nbsp;freesurfer@nmr.mgh.harvard.eduCc:&nbsp;Peled, Noam &lt;NPELED@mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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. &nbsp;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).&nbsp;&nbsp;But you can alias python to be something different in your shell, e.g., here using csh,&nbsp;% alias python python3… or alias to whatever python rev 3 you want to run.&nbsp;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.&nbsp; But typing python at the terminal will run whatever the alias points to. &nbsp;The which command will show you this (CentOS7),&nbsp;% which python/usr/bin/python% python --versionPython 2.7..5% alias python python3% python&nbsp;&nbsp;--versionPython 3.6.8% which pythonpython:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;aliased to python3% /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help&nbsp;&nbsp;--o slicedelayfile&nbsp;&nbsp;--nslices nslices : total number of slices in the volume&nbsp;&nbsp;--order order (up,down,odd,even,siemens)&nbsp;&nbsp;--ngroups ngroups (number of slice groups for SMS)&lt; … rest of output deleted …&gt;% unalias python% which python/usr/bin/python&nbsp;- R.On Oct 29, 2020, at 21:46, Peled, Noam &lt;NPELED@mgh.harvard.edu&gt; wrote:&nbsp;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)?&nbsp;Thanks,Noam&nbsp;From:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;&nbsp;Sent:&nbsp;Thursday, October 29, 2020 9:33 PMTo:&nbsp;freesurfer@nmr.mgh.harvard.eduCc:&nbsp;Peled, Noam &lt;NPELED@mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Noam,&nbsp;The python script&nbsp;/usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e.,&nbsp;$ file /usr/local/freesurfer/dev/bin/slicedelay/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text executable&nbsp;$ which python2/bin/python2$ python2 /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help&nbsp;&nbsp;--o slicedelayfile&nbsp;&nbsp;--nslices nslices : total number of slices in the volume&nbsp;&nbsp;--order order (up,down,odd,even,siemens)&nbsp;&nbsp;--ngroups ngroups (number of slice groups for SMS)&nbsp;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&nbsp;-0.5 (end of the TR).. Used for slice-time correction of fMRI.&nbsp;$ which python3/space/freesurfer/python/linux/bin/python3$ python3 /usr/local/freesurfer/dev/bin/slicedelay --help&nbsp;&nbsp;File "/usr/local/freesurfer/dev/bin/slicedelay", line 9&nbsp; &nbsp;&nbsp;print "USAGE: slicedelay --help";&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;^SyntaxError: Missing parentheses in call to 'print'. Did you mean print("USAGE: slicedelay --help")?&nbsp;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.&nbsp;You can try setting the PATH environment variable such that the first python program found in PATH reports it is version 2.X.&nbsp;- R.&nbsp;On Oct 29, 2020, at 20:47, Peled, Noam &lt;NPELED@mgh.harvard..edu&gt; wrote:&nbsp;/usr/local/freesurfer/dev/bin/slicedelay_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer%E2%80%8B______... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer%E2%80%8B