This is a puzzling problem. Unfortunately I don't have access to a FC4
system to try to recreate what you are seeing.
However, can you edit your make_average_subject/surface/volume scripts
to comment-out these lines (shown here with comment-out chars added):
#set n = `echo $argv | grep -e --help | wc -l`
#if($n != 0) then
# set PrintHelp = 1;
# goto usage_exit;
#endif
#set n = `echo $argv | grep -e --version | wc -l`
#if($n != 0) then
# echo $VERSION
# exit 0;
#endif
This appears to be where your script is stopping, and I would like to
see what it does if it gets beyond this point.
Thanks
On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
> This sounds like a problem I am having, The same script works fine on my
> mac, but not on my FC4 machine. Here is the output, and a message I sent to
> before.
>
> I changed the flags to ³efxv² as Doug recommended, and here is the output
> for make_average_subject, make_average_volume and make_average_surface. The
> script doesn¹t seem to be accepting my command line arguments. I am using
> the current dev version on a Fedora Core 4 system, if that helps.
>
> Thanks,
> Brian
>
> [EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs
> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
> SC036
>
> set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
> $'
> set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp
> $
>
> set PrintHelp = 0 ;
> set PrintHelp = 0
>
> if ( $?SUBJECTS ) then
> if ( 0 ) then
> if ( $?SUBJECTS_DIR ) then
> if ( 1 ) then
> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
> endif
> endif
>
> set average_subject=average
> set average_subject=average
> set ddir = ${SUBJECTS_DIR}/${average_subject}
> set ddir = /apps/freesurfer/subjects/average
> set transform_fname=""
> set transform_fname=
> set XFORM_FLAG=""
> set XFORM_FLAG=
>
> if ( $#argv == 0 ) then
> if ( 27 == 0 ) then
>
> set n = `echo $argv | grep -e --help | wc -l`
> set n = `echo $argv | grep -e --help | wc -l`
> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
> SC032 SC033 SC034 SC035 SC036
> grep -e --help
> wc -l
>
> **
> [EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs
> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
> SC036
>
> set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp
> $' ;
> set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $
>
> set PrintHelp = 0 ;
> set PrintHelp = 0
> set cleanup = 0 ;
> set cleanup = 0
> set transform_fname = talairach.xfm
> set transform_fname = talairach.xfm
>
> if ( $?SUBJECTS ) then
> if ( 0 ) then
> if ( $?SUBJECTS_DIR ) then
> if ( 1 ) then
> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
> endif
> endif
>
> set average_subject = average
> set average_subject = average
>
> set cmdargs = ( $argv ) ;
> set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015
> SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027
> SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
> if ( $#argv == 0 ) then
> if ( 27 == 0 ) then
>
> set n = `echo $argv | grep -e --help | wc -l`
> set n = `echo $argv | grep -e --help | wc -l`
> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
> SC032 SC033 SC034 SC035 SC036
> grep -e --help
> wc -l
>
> **
> [EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs
> --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021
> SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035
> SC036
> set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve
> Exp $' ;
> set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp
> $
>
> set PrintHelp = 0 ;
> set PrintHelp = 0
>
> if ( $?SUBJECTS ) then
> if ( 0 ) then
> if ( $?SUBJECTS_DIR ) then
> if ( 1 ) then
> set SUBJECTS_DIR= ( $SUBJECTS_DIR )
> set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
> endif
> endif
>
> set average_subject=average
> set average_subject=average
> set ddir = ${SUBJECTS_DIR}/${average_subject}
> set ddir = /apps/freesurfer/subjects/average
> set transform_fname=""
> set transform_fname=
> set XFORM_FLAG=""
> set XFORM_FLAG=
>
> if ( $#argv == 0 ) then
> if ( 27 == 0 ) then
>
> set n = `echo $argv | grep -e --help | wc -l`
> set n = `echo $argv | grep -e --help | wc -l`
> echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017
> SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031
> SC032 SC033 SC034 SC035 SC036
> grep -e --help
> wc -l
>
>
>
>
>
>
> From: Doug Greve <[EMAIL PROTECTED]>
> Date: Tue, 27 Sep 2005 15:04:59 -0400
> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] make_average_subject error?
>
>
> Try editing those scripts so that the first line is:
>
> #!/bin/tcsh -efxv
>
> ie, adding "xv"
>
> This turns on all kinds of debugging
>
>
> Brian Schweinsburg, Ph.D. wrote:
> > Re: [Freesurfer] make_average_subject error? Hi Doug,
> > The same thing happens when I try to run them separately. It exits to the
> > prompt with no messages.
> >
> > Brian
> >
> > --
> > Brian C. Schweinsburg, Ph.D.
> > Assistant Adjunct Professor of Psychiatry
> > University of California, San Diego
> > Office: 858-552-8585 x6109
> > Cell: 858-354-3756
> >
> >
> >
> >
> > From: Doug Greve <[EMAIL PROTECTED]>
> > <mailto:[EMAIL PROTECTED]>
> > Date: Tue, 27 Sep 2005 11:16:00 -0400
> > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> > <mailto:[EMAIL PROTECTED]>
> > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] make_average_subject error?
> >
> >
> > Can you run make_average_surface and make_average_volume separately?
> >
> > Brian Schweinsburg, Ph.D. wrote:
> >
> >>
> >> I ran it with make_average_subject --debug \
> >> --subjects SC010 SC012 ...
> >>
> >> I also tried it with --echo. It provides no output.
> >>
> >> I checked the script and it is executable. I looked through the code and
> >> everything seems reasonable given my system except the part that says:
> >> "if person = brian; exit 0"
> >>
> >> Brian
> >>
> >>
> >>
> >>
> >>>
> >>> From: Doug Greve <[EMAIL PROTECTED]>
> >>> <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]>
> >>> Date: Mon, 26 Sep 2005 16:40:48 -0400
> >>> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> >>> <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]>
> >>> Cc: "freesurfer@nmr.mgh.harvard.edu"
> >>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>> <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu>
> >>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>> Subject: Re: [Freesurfer] make_average_subject error?
> >>>
> >>>
> >>> try running it with --debug and send us the output
> >>>
> >>> Brian Schweinsburg, Ph.D. wrote:
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Hi Folks,
> >>>>
> >>>> I tried running the latest make_average_subject script (and the
> >>>> make_average_surface/volume scripts) using the expected command line
> >>>> syntax
> >>>> and after hitting enter it immediately exits to the csh without error,
> >>>> but
> >>>> does not produce anything.
> >>>>
> >>>> make_average_subject --subjects SC010 SC011 SC012 ...
> >>>>
> >>>> I am running the latested dev release with Fedora Core 4.
> >>>>
> >>>> Any ideas as to the problem?
> >>>> Brian
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Freesurfer mailing list
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> Douglas N. Greve, Ph.D.
> >>> MGH-NMR Center
> >>> [EMAIL PROTECTED]
> >>> Phone Number: 617-724-2358
> >>> Fax: 617-726-7422
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> >>
> >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > [EMAIL PROTECTED]
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
>
>
> --
> Brian C. Schweinsburg, Ph.D.
> Assistant Adjunct Professor of Psychiatry
> University of California, San Diego
> Office: 858-552-8585 x6109
> Cell: 858-354-3756
>
>
> > From: Nick Schmansky <[EMAIL PROTECTED]>
> > Date: Fri, 07 Oct 2005 18:04:25 -0400
> > To: Antao Du <[EMAIL PROTECTED]>
> > Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] RE: make_average_surface
> >
> > Add --echo to the command to print its activity, and then send me the
> > output.
> >
> > On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote:
> >> Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out
> >> average_cn, it finished within 1 second without any output and any error
> >> message. I don't know what is wrong. Any helps there?
> >>
> >> I have not updated my freesurface so I downloaded make_average_surface from
> >> a post by Nick in July, 2005.
> >>
> >> Thanks,
> >>
> >> Antao
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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