Brian,
Glad it worked. Clearly that portion of the script needs to be updated for better compatibility.
The messages you are seeing (about nu_8_dxyz.mnc and COR-.info) can be ignored, as they are not errors. In the newest dev release, these messages have been suppressed, because they do not indicate any useful information and give the impression of errors. You do not need to get this new dev release though, as your current release produces valid average surface and volume files.
Nick
On Fri, 2005-10-07 at 16:36 -0700, Brian Schweinsburg, Ph.D. wrote:
Nick, This appears to have done the trick. Make_average_subject ran and created the surfaces. It echos the following error message many times, but I assume this does not matter as it occurs with recon-all as well: INFO: Volume /tmp/mritotal_9750/nu_8_dxyz.mnc cannot be found.
It also specifies the following and created an error log (that later disappeared) saying: INFO: Volume unknown cannot be found. INFO: Volume unknown cannot be found. corRead(): can't open file ./../mri/orig/COR-.info
I assume that this is because I am using mgz files rather than COR? The appropriate volumes were written out in mgz format.
The volumes and surfaces look okay to me.
I included the make_average log file below in case there was something specific that you wanted to see.
Thanks for your help.
Brian
***********make_average log file***************** Fri Oct 7 16:23:33 PDT 2005 /apps/freesurfer/subjects /apps/freesurfer/bin//make_average_volume --out test --subjects SC011 SC012 SC013 setenv SUBJECTS_DIR /apps/freesurfer/subjects SC011 SC012 SC013 mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 mri_convert /apps/freesurfer/subjects/SC011/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 reading from /apps/freesurfer/subjects/SC011/mri/orig.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/SC011/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC011) -------- before --------- 1.078 -0.019 -0.014 0.327; 0.020 1.035 0.187 -11.399; 0.010 -0.185 1.025 -15.094; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC011/mri/orig Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz -------- after --------- 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000;
INFO: Transform Matrix 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000;
Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz --apply_transform /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC012 mri_convert /apps/freesurfer/subjects/SC012/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-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/orig.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/orig-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-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/orig.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-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/orig.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/orig-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/orig-SC013.mgz /apps/freesurfer/subjects/test/mri/orig.mgz mri_convert /apps/freesurfer/subjects/SC011/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 mri_convert /apps/freesurfer/subjects/SC011/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 reading from /apps/freesurfer/subjects/SC011/mri/T1.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/SC011/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC011) -------- before --------- 1.078 -0.019 -0.014 0.327; 0.020 1.035 0.187 -11.399; 0.010 -0.185 1.025 -15.094; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC011/mri/orig Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz -------- after --------- 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000;
INFO: Transform Matrix 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000;
Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz... mri_convert /apps/freesurfer/subjects/SC012/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz --apply_transform /apps/freesurfer/subjects/SC012/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC012 mri_convert /apps/freesurfer/subjects/SC012/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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/T1-SC012.mgz... mri_convert /apps/freesurfer/subjects/SC013/mri/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-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/T1.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/T1-SC013.mgz... mri_average /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC011.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC012.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/T1-SC013.mgz /apps/freesurfer/subjects/test/mri/T1.mgz mri_convert /apps/freesurfer/subjects/SC011/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 mri_convert /apps/freesurfer/subjects/SC011/mri/brain.mgz /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz --apply_transform /apps/freesurfer/subjects/SC011/mri/transforms/talairach.xfm -oc 0 0 0 --devolvexfm SC011 reading from /apps/freesurfer/subjects/SC011/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/SC011/mri/transforms/talairach.xfm... Reading transform INFO: devolving XFM (SC011) -------- before --------- 1.078 -0.019 -0.014 0.327; 0.020 1.035 0.187 -11.399; 0.010 -0.185 1.025 -15.094; 0.000 0.000 0.000 1.000; Trying /apps/freesurfer/subjects/SC011/mri/orig Trying /apps/freesurfer/subjects/SC011/mri/orig.mgz -------- after --------- 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000;
INFO: Transform Matrix 1.078 -0.019 -0.014 0.812; 0.020 1.035 0.187 -11.390; 0.010 -0.185 1.025 -15.089; 0.000 0.000 0.000 1.000;
Reslicing using trilinear interpolation writing to /apps/freesurfer/subjects/test/tmp/make_average_vol-tmp/brain-SC011.mgz... 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 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 nicks@nmr.mgh.harvard.edu Date: Fri, 07 Oct 2005 18:52:12 -0400 To: "Brian Schweinsburg, Ph.D." bschweinsburg@ucsd.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu 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 $VERSION # exit 0; #endif
This appears to be where your script is stopping, and I would like to see what it does if it gets beyond this point.
Thanks
On Fri, 2005-10-07 at 15:24 -0700, Brian Schweinsburg, Ph.D. wrote:
This sounds like a problem I am having, The same script works fine on my mac, but not on my FC4 machine. Here is the output, and a message I sent to before.
I changed the flags to ³efxv² as Doug recommended, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesn¹t seem to be accepting my command line arguments. I am using the current dev version on a Fedora Core 4 system, if that helps.
Thanks, Brian
[bschweinsburg@localhost subjects]$ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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 nicks@nmr.mgh.harvard.edu Date: Fri, 07 Oct 2005 18:04:25 -0400 To: Antao Du antao@itsa.ucsf.edu 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
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