Re: [Freesurfer] RE: make_average_surface

7 Oct 2005


      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
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Re: [Freesurfer] RE: make_average_surface