[Freesurfer] RE: make_average_surface
Hi,
I just installed the newest freesurfer and modified make_average_surface
as suggestion by Nick and Brian. When I run make_average_surface, it stop
with the following error. Did anyone meet the simialr probelm? Thanks
[EMAIL PROTECTED] subjects]$ make_average_surface --subjects AD1293
AD1297 --out average_cn
set VERSION = '$Id: make_average_surface,v 1.14 2005/09/27 19:42:14 greve
Exp $' ;
set VERSION = $Id: make_average_surface,v 1.14 2005/09/27 19:42:14 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= ( /home/antao/freesurfer/subjects )
endif
endif
set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /home/antao/freesurfer/subjects/average
set transform_fname=""
set transform_fname=
set XFORM_FLAG=""
set XFORM_FLAG=
if ( $#argv == 0 ) then
if ( 5 == 0 ) then
set PWD = `getpwdcmd` ;
set PWD = `getpwdcmd`
getpwdcmd
if ( $status ) exit 1 ;
if ( 0 ) exit 1
goto parse_args ;
goto parse_args
set cmdline = ( $argv ) ;
set cmdline = ( --subjects AD1293 AD1297 --out average_cn )
set getting_subjects = 0 ;
set getting_subjects = 0
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ;
set flag = --subjects
if ( ! $getting_subjects ) then
if ( ! 0 ) then
shift ;
shift
endif
endif
switch ( $flag )
switch ( --subjects )
if ( $#argv == 0 ) goto arg1moreerr ;
if ( 4 == 0 ) goto arg1moreerr
set SUBJECTS = $argv[1] ; shift ;
set SUBJECTS = AD1293
shift
set getting_subjects = 1 ;
set getting_subjects = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ;
set flag = AD1297
if ( ! $getting_subjects ) then
if ( ! 1 ) then
switch ( $flag )
switch ( AD1297 )
if ( $getting_subjects ) then
if ( 1 ) then
set SUBJECTS = "$SUBJECTS $argv[1]" ; shift ;
set SUBJECTS = AD1293 AD1297
shift
set getting_subjects = 1 ;
set getting_subjects = 1
else
else
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ;
set flag = --out
if ( ! $getting_subjects ) then
if ( ! 1 ) then
switch ( $flag )
switch ( --out )
if ( $getting_subjects ) then
if ( 1 ) then
set getting_subjects = 0 ;
set getting_subjects = 0
shift ;
shift
endif
endif
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set average_subject = $argv[1] ; shift ;
set average_subject = average_cn
shift
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /home/antao/freesurfer/subjects/average_cn
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( ! $?SUBJECTS ) then
if ( ! 1 ) then
if ( ! $?SUBJECTS_DIR ) then
if ( ! 1 ) then
if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /home/antao/freesurfer/subjects ) then
if ( ! $?FREESURFER_HOME ) then
if ( ! 1 ) then
if ( ! -e $FREESURFER_HOME ) then
if ( ! -e /home/antao/freesurfer ) then
if ( x$transform_fname != x ) then
if ( x != x ) then
goto check_params_return ;
goto check_params_return
echo
echo
echo make_average_surface
echo make_average_surface
make_average_surface
echo
echo
echo input subjects: ${SUBJECTS}
echo input subjects: AD1293 AD1297
input subjects: AD1293 AD1297
echo output subject: ${average_subject}
echo output subject: average_cn
output subject: average_cn
mkdir -p ${ddir} ${ddir}/surf ${ddir}/mri ${ddir}/mri/transforms
${ddir}/mri/T1 ${ddir}/mri/orig ${ddir}/mri/label
mkdir -p /home/antao/freesurfer/subjects/average_cn
/home/antao/freesurfer/subjects/average_cn/surf
/home/antao/freesurfer/subjects/average_cn/mri
/home/antao/freesurfer/subjects/average_cn/mri/transforms
/home/antao/freesurfer/subjects/average_cn/mri/T1
/home/antao/freesurfer/subjects/average_cn/mri/orig
/home/antao/freesurfer/subjects/average_cn/mri/label
if ( -e ${SUBJECTS_DIR}/${average_subject} == 0 ) then
if ( -e /home/antao/freesurfer/subjects/average_cn == 0 ) then
mkdir -p ${SUBJECTS_DIR}/${average_subject}/surf
mkdir -p /home/antao/freesurfer/subjects/average_cn/surf
endif
endif
set tmp_subjects = ( $SUBJECTS )
set tmp_subjects = ( AD1293 AD1297 )
foreach hemi ( rh lh )
foreach hemi ( rh lh )
cd ${SUBJECTS_DIR}/${average_subject}
cd /home/antao/freesurfer/subjects/average_cn
foreach s ( orig white pial inflated )
foreach s ( orig white pial inflated )
echo mris_make_average_surface...
echo mris_make_average_surface...
mris_make_average_surface...
mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg
sphere.reg ${average_subject} $SUBJECTS
mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg average_cn
AD1293 AD1297
reading vertex positions from orig...
processing subject AD1293...
Applying transform.
processing subject AD1297...
Applying transform.
reading icosahedron from /home/antao/
Re: [Freesurfer] RE: make_average_surface
Dear Antao, Check the recent archives with the subject "make_average_subject error?" and the recent exchange with Nick. On Doug's advice, I added 'xv' to the beginning of each make_average* script So, #!/bin/tcsh -efxv Instead of #!/bin/tcsh -ef This produced the output that allowed the freesurfer developers to pinpoint the error. Also on Doug's suggestion, try adding --debug to the make_average_subject command. Nick's recommendation a few posts ago fixed the problem that I was having on a fedora core 4 machine. Based on your initial post, we seem to have similar problems, so give the above suggestions a try. If needed, comment out the offending information in make_average_subject, make_average_volume, and make_average_surface as Nick suggested (if you receive the same error message that I received). Good luck. 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: Antao Du <[EMAIL PROTECTED]> > Date: Fri, 7 Oct 2005 17:27:41 -0700 > To: Nick Schmansky <[EMAIL PROTECTED]> > Cc: Freesurfer Mailing List > Subject: RE: [Freesurfer] RE: make_average_surface > > There is no any output when I add --echo. > > Antao > >> -Original Message- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] Behalf Of Nick >> Schmansky >> Sent: Friday, October 07, 2005 3:04 PM >> To: Antao Du >> Cc: Freesurfer Mailing List >> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] RE: make_average_surface
There is no any output when I add --echo. Antao > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] Behalf Of Nick > Schmansky > Sent: Friday, October 07, 2005 3:04 PM > To: Antao Du > Cc: Freesurfer Mailing List > 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
Re: [Freesurfer] RE: make_average_surface
lvexfm SC012 > mri_convert /apps/freesurfer/subjects/SC012/mri/brain.mgz > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz > --apply_transform > /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 > --devolvexfm SC012 > reading from /apps/freesurfer/subjects/SC012/mri/brain.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > INFO: Applying transformation from file > /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm... > Reading transform > INFO: devolving XFM (SC012) > before - > 1.073 0.022 0.034 0.454; > -0.028 1.071 0.189 -11.925; > -0.034 -0.211 1.188 -18.689; > 0.000 0.000 0.000 1.000; > Trying /apps/freesurfer/subjects/SC012/mri/orig > Trying /apps/freesurfer/subjects/SC012/mri/orig.mgz > after - > 1.073 0.022 0.034 0.401; > -0.028 1.071 0.189 -11.924; > -0.034 -0.211 1.188 -18.687; > 0.000 0.000 0.000 1.000; > - > - > INFO: Transform Matrix > 1.073 0.022 0.034 0.401; > -0.028 1.071 0.189 -11.924; > -0.034 -0.211 1.188 -18.687; > 0.000 0.000 0.000 1.000; > - > Reslicing using trilinear interpolation > writing to > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz... > mri_convert /apps/freesurfer/subjects/SC013/mri/brain.mgz > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz > --apply_transform > /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0 > --devolvexfm SC013 > mri_convert /apps/freesurfer/subjects/SC013/mri/brain.mgz > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz > --apply_transform > /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm -oc 0 0 0 > --devolvexfm SC013 > reading from /apps/freesurfer/subjects/SC013/mri/brain.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > INFO: Applying transformation from file > /apps/freesurfer/subjects/SC013/mri/transforms/talairach.xfm... > Reading transform > INFO: devolving XFM (SC013) > before - > 1.118 -0.032 -0.017 -0.677; > 0.032 1.031 0.204 -17.741; > 0.010 -0.214 1.079 -9.616; > 0.000 0.000 0.000 1.000; > Trying /apps/freesurfer/subjects/SC013/mri/orig > Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz > after - > 1.118 -0.032 -0.017 2.509; > 0.032 1.031 0.204 -17.650; > 0.010 -0.214 1.079 -9.587; > 0.000 0.000 0.000 1.000; > - > - > INFO: Transform Matrix > 1.118 -0.032 -0.017 2.509; > 0.032 1.031 0.204 -17.650; > 0.010 -0.214 1.079 -9.587; > 0.000 0.000 0.000 1.000; > - > Reslicing using trilinear interpolation > writing to > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz... > mri_average > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz > /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz > /apps/freesurfer/subjects/test/mri/brain.mgz > Fri Oct 7 16:29:49 PDT 2005 > make_average_volume done > > > -- > 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 18:52:12 -0400 > > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> > > Cc: Freesurfer Mailing List > > Subject: Re: [Freesurfer] RE: make_average_surface > > > > 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 > > >
Re: [Freesurfer] RE: make_average_surface
/apps/freesurfer/subjects/SC013/mri/orig
Trying /apps/freesurfer/subjects/SC013/mri/orig.mgz
after -
1.118 -0.032 -0.017 2.509;
0.032 1.031 0.204 -17.650;
0.010 -0.214 1.079 -9.587;
0.000 0.000 0.000 1.000;
-
-
INFO: Transform Matrix
1.118 -0.032 -0.017 2.509;
0.032 1.031 0.204 -17.650;
0.010 -0.214 1.079 -9.587;
0.000 0.000 0.000 1.000;
-
Reslicing using trilinear interpolation
writing to
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz...
mri_average
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC012.mgz
/apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC013.mgz
/apps/freesurfer/subjects/test/mri/brain.mgz
Fri Oct 7 16:29:49 PDT 2005
make_average_volume done
--
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 18:52:12 -0400
> To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]>
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] RE: make_average_surface
>
> 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
>>
Re: [Freesurfer] RE: make_average_surface
Can you tell me which OS you are running? Type: cat /etc/redhat-release and uname -a 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
Re: [Freesurfer] RE: make_average_surface
} > 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" > 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> > > <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> > >>> <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 > >>>> > >>>>
Re: [Freesurfer] RE: make_average_surface
t; > > > > 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> > <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> >>> <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 > 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
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] RE: make_average_surface
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
