the subcortical segmentation (Neuron paper) is included in it.
cheers,
Bruce
On Thu, 8 Sep 2005, Stephanie McMains wrote:
Are there other new scripts or features in the dev release other than the
recon-all stuff?
Thanks,
Stephanie McMains
On Sep 8, 2005, at 10:09 AM, Nick Schmansky wrote:
A new set of Linux 'dev' distributions has been uploaded which
contain the recon-all bug fix. That link is:
https://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D
You can either get that new distribution, or just copy the recon-all
taken from Doug's link below to your $FREESURFER_HOME/bin directory.
On Wed, 2005-09-07 at 23:43 -0400, Doug Greve wrote:
That's due to a problem I created a few days ago. Fixes are at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve
doug
On Thu, 8 Sep 2005, Fornito, Alexander wrote:
Hi,
We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz
distribution on our systems, which run Debian 3.1. I noticed that
unpacking the distribution did not place the perl5 directory in
$FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then
downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the
$FREESURFER_HOME/lib/mni/lib directory, and set the environment
appropriately. When I source the environment, I get:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer-dev20050905
FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast
SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects
FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions
MINC_BIN_DIR /usr/local/freesurfer-dev20050905/lib/mni/bin
MINC_LIB_DIR /usr/local/freesurfer-dev20050905/lib/mni/lib
PERL5LIB /usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5
GSL_DIR /usr/local/freesurfer-dev20050905/lib/gsl
QTDIR /usr/local/freesurfer-dev20050905/lib/qt
TCLLIBPATH /usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib
FSL_DIR /usr/local/fsl
However, when I try to run autorecon, I get a message saying "cmd:
Undefined variable." I get this whether the environment is set to link to
perl5 in $FREESURFER_HOME/lib/mni/lib/ or in
/usr/pubsw/packages/mni/current/lib/.
I don't even know if it's the perl library that's the problem. Could
someone please help out? As far as we're aware, all the environments are
set correctly, so we're not sure what Undefined variable is referring to.
The entire output is below:
recon-all -autorecon1 -subjid 27_new -hemi lh
INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905
Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux
########################################
program versions used
$Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version
$
$Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2
2005/03/16 19:02:52 bert Exp $
minctracc.c
$Header:
/software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v
96.11 2004/02/12 05:54:22 rotor Exp $
$Header: /software/source/minc/progs/mincresample/mincresample.c,v
6.12.2.1 2005/03/16 19:02:51 bert Exp $
$Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2
2005/03/16 19:02:49 bert Exp $
$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED]
(i686-pc-linux-gnu) on 2005-08-29 at 19:41:40
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_normalize.c,v
1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_watershed.cpp,v
1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_segment.c,v 1.27
2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15
14:30:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux
PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_tessellate.c,v
1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_smooth.c,v 1.13
2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_inflate.c,v
1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31
2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mris_fix_topology ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id:
mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN
Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
ProgramName: mris_euler_number ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id:
mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN
Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName:
GCC CompilerVersion: 30200
ProgramName: mris_make_surfaces ProgramArguments: -all-info
ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id:
mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User:
UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26
CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_sphere.c,v 1.31
2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_register.c,v
1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mrisp_paint.c,v 1.6
2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_label2label.c,v
1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name:
$ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08
19:45:07 nicks Exp $ User: UNKNOWN Machine: flanders Platform: Linux
PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_em_register.c,v
1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_normalize.c,v
1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_register.c,v
1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion:
$Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_ca_label.c,v
1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: flanders
Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC
CompilerVersion: 30200
#######################################
GCA RB40_talairach_2005-07-20.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.gcs
#######################################
/data/flanders/work/alex/freesurfer/subjects/27_new
Using COR format
---------------------------------------------
MotionCor Thu Sep 8 11:59:54 EST 2005
INFO: no runs were found in
/data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX,
however, there is a volume in
/data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig,
so I am just going to proceed with that as the input.
cmd: Undefined variable.
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