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

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 fsbuild@contbay.com Sent: Thursday, October 29, 2020 9:33 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Peled, Noam NPELED@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 --help USAGE: 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 delay measured 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 <NPELED@mgh.harvard.edumailto:NPELED@mgh.harvard.edu> wrote:

/usr/local/freesurfer/dev/bin/slicedelay

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