Gari,

A little googling tells me that the 'with' statement in python was introduced in python v2.5 in 2008, so unfortunately i think you'll have to update your python version, unless aparcstats2table can be rewritten to not use that statement.

Nick

Hi Nick! this is the version: Centos 4 32b or 64b (x86_64) (Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux)

and the python version is: Python 2.4.3 (#1, Feb 22 2012, 16:05:45) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 (python --version is not working)

thanks! Gari

On Mon, Feb 11, 2013 at 4:50 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

...

Gari,

What OS are you running? is this the Centos 4 32b or 64b (x86_64)?

can you tell me your python version? this way:

python --version

Nick

...

Hi fs experts, I have this error every time I try tu run aparcstats2table :

File "/home/glerma/fs/52/freesurfer/bin/aparcstats2table", line 221 with open(o.qdec, 'rb') as f: ^ SyntaxError: invalid syntax

it appears each time I run aparcstats2table, even when I write: aparcstats2table --help

I have changed the environment variables in order to run the 5.1

version,

...

and it works as always.

What else should I check? thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Gari,

In looking at this further, it seems like that 'with' statement and the dependency on python 2.5 is going to break a lot of systems. So we need to rewrite the script to not use it. In meantime, you can use aparcstats2table from v5.1 (even copy it to your 5.2 bin dir for now).

Thanks for catching this!

Nick

Thanks Nick!! is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another machine, accessing the data from a network drive?

or is it a solution to run the aparcstats2table provided in 5.1 in the same machine, but accessing the data created by the 5.2 version?

many thanks again for your help, Gari

On Mon, Feb 11, 2013 at 5:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

...

Gari,

A little googling tells me that the 'with' statement in python was introduced in python v2.5 in 2008, so unfortunately i think you'll have to update your python version, unless aparcstats2table can be rewritten to not use that statement.

Nick

...

Hi Nick! this is the version: Centos 4 32b or 64b (x86_64) (Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux)

and the python version is: Python 2.4.3 (#1, Feb 22 2012, 16:05:45) [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2 (python --version is not working)

thanks! Gari

On Mon, Feb 11, 2013 at 4:50 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

...

Gari,

What OS are you running? is this the Centos 4 32b or 64b (x86_64)?

can you tell me your python version? this way:

python --version

Nick

...

Hi fs experts, I have this error every time I try tu run aparcstats2table :

File "/home/glerma/fs/52/freesurfer/bin/aparcstats2table", line

221

...

...

...

with open(o.qdec, 'rb') as f:
        ^

SyntaxError: invalid syntax

it appears each time I run aparcstats2table, even when I write: aparcstats2table --help

I have changed the environment variables in order to run the 5.1

version,

...

and it works as always.

What else should I check? thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to

whom

...

...

it is addressed. If you believe this e-mail was sent to you in error and

the

...

...

e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to

you

...

...

in error but does not contain patient information, please contact the sender

and

...

...

properly dispose of the e-mail.

Thanks Doug and Nick, it works now, Gari

On Mon, Feb 11, 2013 at 9:16 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

Gari,

Can you try the attached fixed files? Both aparcstats2table and asegstats2table were fixed.

To install:

cp stats2tab.tar $FREESURFER_HOME/bin cd $FREESURFER_HOME/bin tar xf stats2tab.tar

Thanks again,

Nick

On Mon, 2013-02-11 at 17:06 +0100, Garikoitz Lerma-Usabiaga wrote:

...

Thanks Nick!! is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another machine, accessing the data from a network drive?

or is it a solution to run the aparcstats2table provided in 5.1 in the same machine, but accessing the data created by the 5.2 version?

many thanks again for your help, Gari

On Mon, Feb 11, 2013 at 5:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: Gari,

    A little googling tells me that the 'with' statement in python
    was
    introduced in python v2.5 in 2008, so unfortunately i think
    you'll have to
    update your python version, unless aparcstats2table can be
    rewritten to
    not use that statement.

    Nick


    > Hi Nick!
    > this is the version:
    > Centos 4 32b or 64b (x86_64)
    > (Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06
    EDT 2010
    > x86_64
    > x86_64 x86_64 GNU/Linux)
    >
    >
    > and the python version is:
    > Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
    > [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
    > (python --version is not working)
    >
    > thanks!
    > Gari
    >
    >
    >
    >
    > On Mon, Feb 11, 2013 at 4:50 PM, Nick Schmansky
    > <nicks@nmr.mgh.harvard.edu>wrote:
    >
    >> Gari,
    >>
    >> What OS are you running?  is this the Centos 4 32b or 64b
    (x86_64)?
    >>
    >> can you tell me your python version?  this way:
    >>
    >> python --version
    >>
    >> Nick
    >>
    >>
    >> > Hi fs experts,
    >> > I have this error every time I try tu run
    aparcstats2table :
    >> >
    >> >   File
    "/home/glerma/fs/52/freesurfer/bin/aparcstats2table", line 221
    >> >     with open(o.qdec, 'rb') as f:
    >> >             ^
    >> > SyntaxError: invalid syntax
    >> >
    >> >
    >> >
    >> > it appears each time I run aparcstats2table, even when I
    write:
    >> > aparcstats2table --help
    >> >
    >> >
    >> > I have changed the environment variables in order to run
    the 5.1
    >> version,
    >> > and it works as always.
    >> >
    >> >
    >> > What else should I check?
    >> > thanks!
    >> > Gari
    >> > _______________________________________________
    >> > Freesurfer mailing list
    >> > Freesurfer@nmr.mgh.harvard.edu
    >> >
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >>
    >>
    >>
    >> The information in this e-mail is intended only for the
    person to whom
    >> it
    >> is
    >> addressed. If you believe this e-mail was sent to you in
    error and the
    >> e-mail
    >> contains patient information, please contact the Partners
    Compliance
    >> HelpLine at
    >> http://www.partners.org/complianceline . If the e-mail was
    sent to you
    >> in
    >> error
    >> but does not contain patient information, please contact
    the sender and
    >> properly
    >> dispose of the e-mail.
    >>
    >>
    >