Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

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falk.luesebrink＠med.ovgu.de

25 Jan 2019 25 Jan '19

4:26 a.m.

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

[klinikum_logo_schmal_e-mail_blau] Universitätsklinik für Neurologie

Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de http://www.kneu.ovgu.de/kneu.html

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Juergen Haenggi

25 Jan 25 Jan

4:34 a.m.

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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

----------------------------------------------------------------------------------------------------- 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 mailto:falk.luesebrink@med.ovgu.de http://www.kneu.ovgu.de/kneu.html http://www.kneu.ovgu.de/kneu.html

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

falk.luesebrink＠med.ovgu.de

4:41 a.m.

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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

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.chmailto:j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)

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

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.demailto:falk.luesebrink@med.ovgu.de http://www.kneu.ovgu.de/kneu.html

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Lars.Dinkelbach＠med.uni-duesseldorf.de

4:57 a.m.

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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

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

# 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

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.

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.chmailto:j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)

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

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.demailto:falk.luesebrink@med.ovgu.de http://www.kneu.ovgu.de/kneu.html

Bruce Fischl

10:06 a.m.

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

Hoopes, Andrew

11:24 a.m.

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 > > > > >

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participants (5)

Bruce Fischl
falk.luesebrink＠med.ovgu.de
Hoopes, Andrew
Juergen Haenggi
Lars.Dinkelbach＠med.uni-duesseldorf.de