Do you mean you're not sure if it will work?
-----Original Message-----
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 9/9/2005 9:28 AM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intstallation problems on new dev?
You should be able to run it with -autorecon-all -rerun. Having said
that, I don't know that we've actually run it that way.
doug
Fornito, Alexander wrote:
Hi Bruce and Doug,
When you say it can be done automatically,does that mean it
wouldn't require additional editing? Does it use edits that are already
performed (eg., in creating surfaces with the dev version)?
If so, do you know how long it would roughly take to re-create
them in this way?
Thanks again,
Alex
-----Original Message-----
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 9/8/2005 10:45 PM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Intstallation problems on new
dev?
Hi Alex,
you probably want to regenerate everything. Note that this can
be done
automatically through recon-all (Doug can tell you the
switches).
cheers,
Bruce
On Thu, 8 Sep 2005, Fornito, Alexander wrote:
Seems to be working now. Thanks Doug, you're a
lifesaver!!
As an aside, will surfaces created using the 20050509
dev version be compatible with those created using the upcoming stable release?
-----Original Message-----
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Thu 9/8/2005 1:43 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intstallation
problems on new dev?
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.
>
>
>
_______________________________________________
> 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
