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Dear all,

I am getting the same problem on ubunto 18.04 without WSL. I would be glad for advice how to fix it.

Best,
Lars
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "falk.luesebrink@med.ovgu.de [falk.luesebrink@med.ovgu.de]
Gesendet: Freitag, 25. Januar 2019 10:41
An: Freesurfer Mailinglist
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

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Dear Juergen,

 

Thanks for your quick reply! Actually the spelling error is in the error message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes

 

# extensive error checks

#    if options.fsgd is None and

    if options.qdec is None:

#        print 'ERROR: Specify --fsgd or --qedc'

        parser.print_help()

        print '\nERROR: Specify --qedc (and other required arguments)\n'

        sys.exit(1)

 

#    if options.fsgd is not None and options.qdec is not None:

#        print 'ERROR: Specify either --fsgd or --qedc, not both'

#        sys.exit(1)

 

At least Martin is consistent with his typo. :D

 

Best,

Falk

 

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

 

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Dear Falk

 

I have no idea, but recognised that the error refers to --qedc and not to --qdec.

maybe there is a spelling error somewhere that is related to your problem.

 

HTH

Cheers

Jürgen

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On 25 Jan 2019, at 10:26, falk.luesebrink@med.ovgu.de wrote:

 

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Dear all,

 

Has anyone run the longitudinal pipeline successfully using the WSL? I’m running it with Ubuntu 18.04.1 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

 

I’m trying to process my first longitudinal data set following the instructions of the tutorial as close as possible. The data has been processed without issues and now I want to do the statistical analysis. When I run:

long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR

 

I get the following error:

File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448

    print '\nERROR: Specify --qedc (and other required arguments)\n'

                                                                   ^

SyntaxError: invalid syntax

 

I get comparable errors for any other long_* command I try to run, e.g. long_qdec_table with or without any arguments gives:

File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119

   print '\nERROR: Specify --qedc'

                                  ^

SyntaxError: Missing parentheses in call to 'print'. Did you mean print('\nERROR: Specify --qedc')?

 

Does anyone have a clue where this error originates from using either WSL or Ubuntu 18.04?  

 

Best,

Falk

...............................................

 

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