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
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
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 greve@nmr.mgh.harvard.edu Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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 greve@nmr.mgh.harvard.edu Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu 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
Hi Doug, The same thing happens when I try to run them separately. It exits to the prompt with no messages.
Brian
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:
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 greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: "freesurfer@nmr.mgh.harvard.edu" 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 <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu> Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." <bschweinsburg@ucsd.edu> <mailto:bschweinsburg@ucsd.edu> 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? 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 greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu 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
Hi Doug, I changed the flags to ³efxv² as you recommend, 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
[bschweinsburg@localhost 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 $argv | grep -e --help | wc -l` echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 grep -e --help wc -l
** [bschweinsburg@localhost subjects]$ 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 greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 15:04:59 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu 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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Tue, 27 Sep 2005 11:16:00 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu 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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Date: Mon, 26 Sep 2005 16:40:48 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu mailto:bschweinsburg@ucsd.edu 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 greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu 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
freesurfer@nmr.mgh.harvard.edu
-
Brian Schweinsburg, Ph.D. -
Doug Greve