I changed the flags to “efxv” as you recommend, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesn’t 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
