I believe this python2 issue has been fixed in the dev version found here https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mri...
best, Andrew
On 1/25/19, 10:08 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Falk
thanks for catching the typo. I fixed it - nice to have an easy thing to fix for a change :)
Bruce
On Fri, 25 Jan 2019, falk.luesebrink@med.ovgu.de wrote:
> > External Email - Use Caution > > 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 > > > > External Email - Use Caution > > 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 > > ----------------------------------------------------------------------------------------------------- > > University of Zurich > > Dr. Jürgen Hänggi, Ph.D. > > Department of Psychology > > Division Neuropsychology > > Binzmuehlestrasse 14, PO Box 25 > > 8050 Zurich, Switzerland > > > > 0041 44 635 73 97 (phone office) > > 0041 76 445 86 84 (phone mobile) > > 0041 44 635 74 09 (fax office) > > BIN 4.D.04 (office room number) > > > > j.haenggi@psychologie.uzh.ch (email) > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > http://www.juergenhaenggi.ch (private website) > > > > This email (and any attachment/s) contains confidential and/or privileged > > information. If you are not the intended recipient (or have received this > > email in error) please notify the sender immediately and destroy this > > email. Any unauthorised copying, disclosure or distribution of the > > material in this email is strictly forbidden. > > ----------------------------------------------------------------------------------------------------- > > > > > > > > On 25 Jan 2019, at 10:26, falk.luesebrink@med.ovgu.de wrote: > > > > External Email - Use Caution > > > > 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 > > ............................................... > > > > <image001.gif> > > Universitätsklinik für Neurologie > > > > Otto-von-Guericke-Universität Magdeburg > Medizinische Fakultät > Leipziger Str. 44 > 39120 Magdeburg > > > > Telefon: +49-391-6117-512 > > falk.luesebrink@med.ovgu.de > http://www.kneu.ovgu.de/kneu.html > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >